Human vs. Machine-Enhanced Scientific Discovery – CDD Webinar VideoSeptember 27, 2016-We’re delighted to share with you the video from our exciting recent “Human vs Machine-Enhanced Scientific Discovery” Webinar: The panelists peered into a rapidly approaching future world where computers are doing experiments side-by-side with scientists. In that reality, having data that is FAIR (Findable, Accessible, Interoperable, and Reusable) is critical. The panelists reframed the way we [...]
CDD Vault Powers Virtual Pharma Distributed Drug DiscoverySeptember 22, 2016-Dr. Mike Pollastri spent almost a decade as a research scientist in Big Pharma (Pfizer) before turning to academia and today he is running one of the best known neglected disease research labs at Northeastern University. Mike generously is sharing this slide set which he presented at the 250th meeting of the ACS 2015 so that others who think they can not afford to run drug discovery consider this economical distributed, virtual model....
CDD Vault Update: Cancel ExportSeptember 9, 2016-Today's release brings several usability enhancements to help you get data in to and out of your vault smoothly. Notably, we added an option to cancel an export, added support for European date formats, and made a couple of additions to the API.
Spotlight Interview with Dr. Andrew Calabrese – VP of Chemistry at AgriMetisSeptember 6, 2016-Going from academic research to industrial research, came with the realization that bulk data drives industrial research, whether its pharmaceuticals or agrochemicals. In academia you might focus in on a very specific issue and track data very carefully, on individual data points. In industry it's all about bulk data, and it's about drawing plots of multiple compounds vs multiple data points, and trying to find correlations and find the outliers and find the reason why compounds are doing what they're doing. CDD Vault is a great tool for bulk data analysis...
CDD to Present and Exhibit at the 14th Annual Discovery on Target in Boston (September 19-22)August 29, 2016-CDD will be presenting scientific talks and exhibiting at the upcoming Discovery on Target conference in Boston, between September 19th and 22nd, 2016. Come visit us in Booth 42 CDD will be exhibiting the latest developments in our hosted solution for chemical registration, bioassay data management, Structure Activity Relationship (SAR) analysis, calculations, inventory, and visualization [...]
CDD Vault Update: Software Upgrade Part 2August 19, 2016-Today's release brings another major upgrade to the software stack that CDD Vault runs on. This allows us to maintain good application security and paves the way for upcoming features. It was a massive amount of work, but if we did everything right you won't notice a difference. In addition we increased performance and introduced several small enhancements.
Human vs. Machine-Enhanced Scientific DiscoveryAugust 10, 2016-Join Mark Musen (Stanford), Janice Kranz and Stephan Schürer (University of Miami) for CDD’s Q3 Town Hall Webinar, “Human vs. Machine-Enhanced Scientific Discovery” We’re seeing ‘Big Data’ everywhere: healthcare, business, sports, traffic control, biology, drug discovery. The ‘behind-the-scenes’ tool enabling the power of Big Data – searching, sharing, visualizing, querying, analyzing – is the Semantic Web (aka ‘Web 3.0’)[1]. [...]
BioAssay Express (a bit of an unveil)August 4, 2016-CDD's BioAssay Express software allows you to convert human readable bioassays into machine readable, marked up text. The technology has been tested on over 3000 "best of Pubchem" MLPCN assays. New insights and patterns can be seen around the widely shared "probe" compounds to further validate the utility of the approach. With the Common Assay Template, we've tried to make good subjective calls regarding the most important parameters influencing bioassays, whilst keeping a minimum number of categories. However, it is worth emphasizing that the underlying technology can be used with any templates, terms, and ontologies (i.e. yours). As a matter of focus, we've focused this new technology on bioassays. In contrast to our polished, professional CDD Vault platform, Bioassay Express is still a relatively new technology, yet clearly it does work. For those interested in collaborations or evaluations please send an email to info@collaborativedrug.com if you'd like to try using this technology with your own protocols (behind firewall, online in Bioassay Express, or potentially integrated with CDD Vault)...
Share Your Delight With CDD While Helping Fund Neglected Disease R&DJuly 12, 2016-CDD has teamed up with David Swinney’s colleagues at iRND3 and you to introduce a CDD Vault Referral Program that simultaneously raises money for their non-Profit Neglected Disease Research. The Institute for Rare and Neglected Diseases Drug Discovery (iRND3) is not only a partner for our referral program, they are also a very active CDD [...]
Top Ten Reasons Academic Research Laboratories Need CDD VaultJuly 12, 2016- Top Ten Reasons Academic Research Laboratories Need CDD Vault
Students come and go, but data live on
Students learn about data management and analysis tools
Management of research workflow is enhanced
Graduates’ job prospects are enhanced
Chemistry and Biology students learn about cross-disciplinary teams
Structure-activity analyses are enhanced
Research collaborations are promoted
New Leads and other IP values are enhanced
Students and researchers can focus on science, not maintaining datasystems
Affordable, budgeted cost instead of expensive in-house datasystems
GSK’s Kinetoplastid Research Data Set Available FREE Within CDD VaultJuly 12, 2016-In an effort to fuel open-source research and drug discovery in Kinetoplastid diseases, GSK Tres Cantos and CDD have assembled three Kineto Boxes containing 592 New Small Molecules. Using parallel whole-cell phenotypic assays, the GSK HTS diversity set of 1.8 million compounds was screened against the three kinetoplastids most relevant to human disease, i.e. Leishmania [...]
Genentech & UCSF Library Selection – CDD Webinar VideoJune 1, 2016-CDD’s May Town Hall Webinar explored how the selection of optimal chemical libraries can improve the drug discovery process. Guided by a distinguished panel of speakers, this Town Hall style webinar challenged our panelists, as well as the audience, to think hard about what should be included in an optimal small molecule library and to [...]
CDD to Present at the World Preclinical Congress – Mastering Medicinal Chemistry Conference in Boston (June 15-17)May 25, 2016-CDD will be presenting scientific talks, posters and exhibiting at the upcoming World Preclinical Congress Mastering Medicinal Chemistry conference in Boston, between June 15th and 17th, 2016. Anna Spektor, CDD’s Customer Success Manager, and Shirley Louise-May, CDD Advocate, will be presenting a talk and 2 posters: “CDD Vault: Activity, Registration, Visualization, Collaboration” “CDD Vision: A [...]
Genentech & UCSF Ponder Optimal Library Selection for Drug DiscoveryMay 5, 2016- Join us for CDD’s 2nd Town Hall Webinar, “Optimal Library Selection for Drug Discovery” Researchers agree that selecting the best libraries for optimizing their drug discovery is a vital part of the process. Unfortunately, this is likely where most agreement ends. Even the idea that scientists should avoid so-called “Dark Chemical Matter” compounds seems [...]
CDD TOWN HALL WEBINAR VIDEO: DRUG DISCOVERY PUBLIC-PRIVATE PARTNERSHIPS (PPPs)April 19, 2016-CDD’s inaugural CDD Town Hall Webinar explored how Public-Private Partnerships (PPPs) have inspired efforts to improve the pace of drug discovery. Guided by a distinguished panel of speakers, this Town Hall style webinar examined: Various approaches for establishing successful PPPs How PPPs have affected the drug discovery efforts for Commercial and Neglected Tropical Diseases The [...]
CDD Vault Update: Design RefreshApril 14, 2016-This release provides a visual refresh to CDD Vault, plus navigational cleanup and simplification. Design The new design greets you on the log-in page, and is applied throughout the site. We’ll let it speak for itself, but we hope you like it as much as we do. New Settings Page All settings have been consolidated [...]
CDD Spotlight Interview with James Moe – President, CEO and a co-founder of OligomerixApril 14, 2016-“We’re using CDD Vault as a way of storing our chemical structures, as a way of searching them, as a way of storing all of our assay data. We’re also using it for doing calculations, for analyzing our data, for creating reports and communicating the data to others, and then also, very importantly, for working [...]
Celebrating A Dozen Years of Collaborative Drug Discovery in CDD Vault: 12 Popular PostsApril 6, 2016-To commemorate a dozen years of trusted, secure data hosting by leading drug discovery project teams in CDD Vault, we're sharing a dozen popular recent posts:
1. Why using pIC50 instead of IC50 will change your life (9304 Views - 14 July 2014). Video posted on Apr 15 2015: https://www.collaborativedrug.com/buzz/2015/04/15/on-demand-video-from-the-pic50-scientific-webinar/
2. New Data from the FDA Available for Public Access Use (1504 Views - 30 April 2011)
3. New White Paper: Promoting Effective Project Teams for Drug Discovery (1492 Views - August 6 2015)
4. CDD First Live Webinar Event - Are Your Compounds Biased by Your Discovery Techniques (with Christopher Lipinski and Matthew Soellner...
CDD Spring Tour – ADDC, EB, ASPET, BioIT, UCSD, PPPMarch 18, 2016-“Spring is the time of plans and projects.” -Leo Tolstoy In Anna Karenina, Leo Tolstoy wrote that “Spring is the time of plans and projects.” How Leo knew of CDD Vault’s collaborative Project design is beyond us, but he was correct in asserting that Spring is the time to plan on joining CDD as we [...]
Valuable New ASINEX Libraries Now in CDD VaultMarch 10, 2016-How can your early drug discovery program be more efficient? Have you ever screened ASINEX compounds? Did you know you can view ASINEX, and other leading vendor, libraries directly in CDD Vault? CDD has a long-standing partnership with ASINEX going back more than 10 years. Together we provide innovative offerings for drug discovery scientists that [...]
Seminar: Lunchtime with Collaborative Drug DiscoveryMarch 9, 2016-Join us for a lunchtime seminar at the University of California in San Diego (UCSD) Wednesday, April 6, 2016 10:00 am – 2:00 pm PT Register for and join our free seminar to learn how local researchers are applying research informatics to their chemical and biological experiments. You will learn about chemical registration, data archival, [...]
CDD to Attend the Academic Drug Discovery (ADDC) UK Workshop 2016 (March 22nd – 23rd, 2016)March 7, 2016-CDD will be attending the upcoming Academic Drug Discovery (ADDC) UK Workshop at the Cripps Court Magdalene College in Cambridge, United Kingdom, on March 22nd & 23rd, 2016. CDD will be available to discuss the latest developments in CDD Vault, our hosted solution for chemical registration, bioassay data management, Structure Activity Relationship (SAR) analysis, calculations, [...]
CDD Vault Update: Introducing New Inventory for CDD VaultFebruary 27, 2016-Have you ever gone to the storage freezer to get a stock compound, only to discover that the vial is empty? Assuming you found the vial at all? Or have you spent the afternoon trying to track down a compound, wondering to yourself if there’s an app for that? And if you work in the [...]
CDD Town Hall Webinar: Public-Private Partnerships (PPPs) for Drug DiscoveryFebruary 24, 2016- SAVE THE DATE for CDD’s inaugural Town Hall: What are Public-Private Partnerships for Drug Discovery? In recent decades, the proliferation of world-wide epidemics and health emergencies (such as HIV, MERS, Ebola, and most recently Zika) has inspired efforts to improve the pace of drug discovery through large-scale collaborations. So-called Public-Private Partnerships (PPPs) have been [...]
CDD to Present at 3rd Annual Medicinal Chemistry Strategy Round Table Meeting in the United Kingdom (9th March, 2016)February 23, 2016-CDD will be speaking in and facilitating interactive and informal discussions at the upcoming Medicinal Chemistry Strategy Meeting in the United Kingdom, on March 9th, 2016. CDD will also be available to discuss the latest developments in CDD Vault, our hosted solution for chemical registration, bioassay data management, Structure Activity Relationship (SAR) analysis, calculations, and [...]
CDD Vault Update: Software UpgradeFebruary 12, 2016-Today’s release brings a major upgrade to the software stack that CDD Vault runs on top of. This allows us to maintain good application security and paves the way for upcoming features. It was a massive amount of work, but if we did everything right you won’t notice a difference. Overwrite a saved search One [...]
CDRD Chooses CDD for New Drug Discovery Informatics PlatformFebruary 11, 2016-Press release BURLINGAME, CA and VANCOUVER, BC (February 11, 2016) — Collaborative Drug Discovery (CDD) today announced that The Centre for Drug Research and Development (CDRD) has chosen CDD Vault to replace their Drug Discovery Informatics Platform. After in-depth evaluation of leading systems, CDRD decided on the CDD Vault platform. CDD Vault is a hosted [...]
How can the collaborative scientific community be proactive and more agile – not just for Zika virus, but also for the next epidemic around the bend?February 5, 2016-From the desks of Sean Ekins, CSO and Barry Bunin, CEO
You would have to be hiding under a rock to have not heard about the Zika virus which is being found in the Americas and spreading globally as people travel. The Zika virus, carried by one of humanity’s long-term pests the mosquito, so far appears to be capable of being sexually transmitted, as well as transmitted with blood transfusions and by birth. It has also recently been found in urine and saliva. There have been large numbers of children born with microcephaly which has been associated with the virus though this is not firm since causality has not been proven, yet the correlative relationship appears strong. We currently cannot predict what scientific discovery or epidemiological finding will be made next or how this will unfold.
It is pretty clear...
CDD Super Bowl SundayFebruary 1, 2016-As the Super Bowl marches into CDD's backyard, we also have an internal competition heating up.
This has nothing to do with the performance of the Broncos, Panthers, Cardinals, or Patriots - but rather the fierce competition of prioritizing informatics functionality to expedite drug discovery research.
In the Eastern Conference, Visualization-Calculations matched up against Inventory needs.
And in the Western Conference, it was...
Top Ten Reasons for Biotechs to Acquire CDD VaultJanuary 12, 2016-Top Ten Reasons for Biotechs to Acquire CDD Vault Scientists may come and go, but data live on Encourage project scientists to follow healthy data management practices Enhance research workflows Improve acquisition and analysis of project data Serve all members of the project team Promote research collaborations Enhance structure-activity analyses Protect New Leads and other [...]
CDD to Present at SLAS 2016 National Meeting in San Diego (Jan 25-27)January 5, 2016-CDD will be presenting three scientific talks at the upcoming Society for Laboratory Automation and Screening (SLAS) Conference in San Diego, between January 25th and 27th, 2016. Dr. Sean Ekins, CSO at CDD, will be presenting a talk, “Ensuring Chemical Structure, Biological Data and Computational Model Quality” Dr. Barry Bunin, CEO of CDD, will be [...]
Dark Chemical Matter in Drug Discovery: When Compounds Simply Won’t WorkDecember 7, 2015-Over the years, thousands and thousands of compounds have been tested over an ever-increasing number of targets and assay conditions. And while it is expected to find most compounds in screening exercises to be inactive, nobody previously had investigated if there were any compounds that would be inactive against any target/assay used to date.
Well, Novartis addressed this question in a recent publication in Nature Chemical Biology. In this study, the authors looked into the Novartis screening deck and the NIH’s Molecular Libraries collection, identified those compounds that were inactive in at least 100 assays (Novartis: 234 assays; NIH: 429 assays), and coined a new label for these compounds: Dark Chemical Matter (DCM).
This study brings to light that there are compounds that for unknown reasons are simply inactive in many biological assays. Clearly, robust database software with assay analytical and data visualization capabilities like those found in CDD Vault and CDD Vision help rapidly ID activity cliffs. Yet, with any tools, perhaps the darkness associated to compounds can be better understood over time as a function of the type of assay, target pursued, and biological assay conditions.
Who is to say that one of these dark compounds wouldn’t be active in an assay in some other research group or company...
CDD Vault Update: Usability enhancementsDecember 4, 2015-This release introduced several handy enhancements to CDD Vault: streamlined Explore Data sidebar supporting projects between vaults, color-coded plate summary statistics on the Run Summary tab, streamlined project membership interface, and streamlined sharing and removal of resources in projects. We have also added keyword searching for solvent data.
Lights, Camera, Action…CDD Vault Hits the Red Carpet!December 2, 2015-In this fast-paced action-packed video, the researchers at the Martin Research Group take us on an epic quest for knowledge. You’ll share their struggles, feel their pains and celebrate their victories as CDD Vault helps Michael and his lab mates locate the available chemical derivatives for a proposed Alzheimer’s treatment. This nail-biting journey will take [...]
Drug Discovery Thought Leadership Webinar: Review, Summary, Follow-up and RecordingsNovember 17, 2015-On November 4th, 2015, CDD hosted a live webinar where thought leaders discussed the challenges of modern drug discovery. For those who could not attend, we invite you to review this summary and follow these links to the webinar recordings. Panelists’ discussion: Retrospective analysis can be useful for limited domains, yet lessons are often not [...]
Videos on Changes in Drug Discovery Thought Leadership WebinarNovember 11, 2015-Our recent CDD Webinar by industry thought leaders with the scientific community discussed why innovation and synergy are critical to drug discovery project team success is now live online.
CDD was joined in the discussion by:
* Daniel Erlanson (President), Carmot Therapeutics
* Mark Gurney (CEO), Tetra Discovery Partners
* Henry Johnson (Principal Scientist), Kezar Life Sciences
* Shirley Louise-May (CDD Advocate), ex-Pfizer
* Nicholas Skelton (Principal Scientist), Genentech
Our previous CDD Webinar case study with viDA Therapeutic’s Dr. Dale Cameron on how innovation and synergy was implemented...
CDD Presents at the International Chemical Congress of Pacific Basin Societies in Honolulu, Hawaii, in December 2015November 5, 2015-CDD presents talk and poster at the 2015 International Chemical Congress of Pacific Basin Societies in December Aloha! CDD will be attending and presenting at the 2015 International Chemical Congress of Pacific Basin Societies. This conference is scheduled for December 15-20, 2015, in Honolulu, Hawaii. The PacifiChem Congress will be held at the Hawaii Convention [...]
Ninth Chapel Hill Pharmaceutical Sciences Conference – Frontiers in chemical biology: transforming drug discoveryOctober 16, 2015-CDD co-sponsored conference meeting summary
From the desk of Sean Ekins, CSO
Yesterday I attended the Ninth Chapel Hill Pharmaceutical Sciences Conference which was co-sponsored by CDD. I was not alone as there was a large audience of graduate and post graduate students and professors, easily in excess of 250.
We were treated to 8 exceptional talks from luminaries in the field of chemical biology as follows.
Kevan Shokat (UCSF) – Nontraditional approaches to drugging traditional targets: kinases and GTPases
Tom Muir (Princeton University) – Painting Chromatin with synthetic protein chemistry
Donald McDonnell (Duke University) – ERRα regulated lactate metabolism contributes to resistance to targeted therapies in breast cancer
Bryan Roth (UNC at Chapel Hill) – Exploring the subterranean biology of known drugs...
CDD Vision Update: HistogramsOctober 12, 2015-This update brings histograms to CDD Vision, and more flexibility in setting scatter plot scale ranges.
CDD Webinar: Industry Leaders Discuss the Challenges of Modern Drug DiscoveryOctober 11, 2015-CDD proudly invites you to discuss how our fields are evolving with industry thought leaders. CDD will explore the rate of evolution of our communities current understanding and state of the art of Biology, Chemistry and Software. Gene drive, molecular machines, semantic web - looking into the future sheds light on the present. Exploring these trends should be provocative for the forward-thinking drug discovery researcher.
Members of CDD's customer advisory board will be available to discuss their perspectives plus interactive Q&A with the scientific Community. CDD previously announced following industry thought leaders were carefully selected to help guide the short-term and long-term development of the CDD Vault platform with the broader scientific community:
On Demand Video from the Wrangling all your Diverse Assay Data WebinarOctober 8, 2015-CDD’s recent live webinar event, Wrangling all Diverse Assay Data, was a great success. To summarize, Dr. Dale Cameron discussed how viDA Therapeutics implemented CDD Vault, saving time and money by leaving behind the “large amount of labor it took” to maintain multiple tools. This webinar demonstrated firsthand how a hosted, secure collaborative system makes [...]
From the desk of CDD Vault’s early customer Professor James McKerrowOctober 6, 2015-The 2015 Nobel Prize in Physiology or Medicine was awarded to three scientists who pioneered the search for drugs to treat neglected tropical diseases (NTDs). Their efforts parallel and validate the commitment of CDD to provide computational searches and database management in support of research targeting these diseases of global health importance.
William C Campbell and Satoshi Omura shared one half of the 2015 Nobel Prize for their discovery and development of avermectin and its analog ivermectin. Ivermectin has played a major role in stopping the transmission of River Blindness in the New World and lymphatic filariasis throughout the tropical world. Youyou Tu was awarded the other half of the Nobel Prize for her discovery of artemisinin, the current drug of choice for malaria. The recognition of the work of these scientists by the Nobel Committee is validation to the efforts of CDD and their global partners in addressing the need for drugs, vaccines, and diagnostics to control, and perhaps someday eliminate, neglected tropical diseases. In fact CDD was launched in 2004 as a spinout of Eli Lilly with the Director of the Sandler Center for Basic Research in Parasitic Diseases at the University of California San Francisco as a key early customer foreshadowing our growth over the last decade for neglected and commercial drug discovery...
Nobel Prize for neglected parasitic diseases: Could it spur more treatments?October 5, 2015-CDD is committed to working on neglected diseases for no other reason than because it is the ethical and right thing to do. Every year millions of our brothers and sisters around the world perish because they happen to live in a region where parasites, bacteria or viruses coexist for which treatments are not accessible, too expensive, too toxic, or worse still, they just have not been discovered. It seems almost too medieval to think that people are dying in the millions because of the equivalent of modern day plagues brought on by microscopic entities that have surrounded us in some cases for millennia.
Today we celebrate 3 scientists who made a dent in some of these diseases. William Campbell and Satoshi Omura won for their work on discovering Avermectin which lead to treatments for River Blindness and Lymphatic Filariasis. Youyou Tu also won for her work on Artemisinin as a treatment for malaria...
CDD To Attend the 2nd Annual Oxford Global Drug Discovery USA Congress in October 2015 in Boston, MASeptember 30, 2015-CDD will attend and exhibit at the Oxford Global Drug Discovery USA Congress on October 29th and 30th, 2015 at The Westin Boston Waterfront Hotel in Boston, MA. Come visit us in Booth 3. CDD will be exhibiting the latest developments in our hosted solution for bioassay data management, chemical registration, and Structure Activity Relationship [...]
For 3D Vision, Mine PDB Ligand Structures in CDD Vault (Part 2 of 2)September 28, 2015-For 3D Vision, Mine PDB Ligand Structures in CDD Vault Guest blog from CDD Advocate: Dr. Dale Cameron Part 2 of 2 In a recent blog post, CDD announced the addition of the latest ligand structures from the Protein Data Bank (PDB) into the CDD Vault®. The expanded availability of this unique and useful data is indeed [...]
CDD Spotlight Interview with Ronnett Seldon, University of Cape Town, South AfricaSeptember 15, 2015-Interviewed by Collaborative Drug Discovery, Inc.
When you joined H3-D were they already using CDD Vault?
Yes, CDD Vault is a central database so everybody has access to the data. I have been with the project for 18 months now, and I run a dose-response inhibition assay which generates a significant amount of data analysis. I had intended to use GraphPad prism or Stata for my analysis in which I have to define controls and use a 4 parameter logistic regression for the curve generation. For large data sets, this takes a lot of time. I am a clinical research microbiologist, so I have a fair amount of experience with large datasets.
While uploading data to CDD, I noticed in the help section of CDD Vault that the platform has a customized 4-parameter logistic regression that is used to process and analyze the data. This has changed, a whole lot and for the better, the amount of time I need to upload and process the data. CDD Vault is not just a database to which I bulk upload data, but I actually use it to analyze and process all my data...
You need a new database for your chemistry and biology data – but you wonder if the switch will be too much work?September 9, 2015-From the desk of Dr. Sylvia Ernst, Head of Sales and Sales Operations:
"CDD Vault makes it easy and the CDD team will help ensure a smooth transition"
How, you ask? What should you do when you really need to modernize your biology and chemistry data management, and yet the change feels like a colossal task? Let’s shed some light on the concerns we’ve heard and maybe the update will be easier than you imagined.
Concern #1: We have so much legacy data which we continue to use. How can we get the existing data quickly into new, improved systems and processes?
Concern # 2...
Want 3D Vision? Protein Data Bank (PDB) Ligand Structures are now LIVE in CDD Vault® (Part 1 of 2)August 26, 2015-PDB ligand structures are now LIVE in CDD Vault®
Guest blog from CDD Advocate: Dr. Dale Cameron
The very best medicinal chemists can think in 3D about the compounds they design (both in the absence and presence of a molecular target). They appreciate that 3D structures are dynamic, dependent on their environment and important for optimizing candidate properties.
Ligand-target co-crystallization data can augment traditional structure activity relationship analyses. Now you can collectively consider your proprietary data within CDD Vault® using the latest ligand structures from...
CDD Vault Webinar: Wrangling all your Diverse Assay DataAugust 20, 2015-Online Webinar: Wed Sept 30th at 9am PT, noon ET, 4pm GMT
A collaborative webinar by Dr. Dale Cameron (viDA Therapeutics) with Dr. Barbara Holtz and Charlie Weatherall
Have you ever wondered about the cost vs benefits of a shared resource for your full project team? What are the benefits versus sharing excel files or traditional databases for screening biologists, medicinal chemists, and other key collaborators? How can it work?
Find out how viDA Therapeutics (and you) can save time and money relative to the "large amount of labor it took" to maintain multiple tools. How did a project team go from starting out using just flat files to mach-6 with CDD Vault. Why was it the right solution and the right time? Why did they buy? How did it work and even exceed expectations?
See first-hand how a hosted, secure collaborative system makes information available for...
CDD To Attend the Frontiers in Medicinal Chemistry Conference in September 2015 in Antwerp, BelgiumAugust 20, 2015-CDD will attend and exhibit at the Frontiers in Medicinal Chemistry Conference on September 14-16, 2015 at the University of Antwerp (City Campus) in Antwerp, Belgium. Come visit us at our booth. CDD will be exhibiting the latest developments in our hosted solution for bioassay data management, chemical registration, and Structure Activity Relationship (SAR) analyses. [...]
CDD Vault Update: Visualize Many Plots, Transcend your VaultAugust 14, 2015-This release introduces more projects in CDD Vault, and more plots in CDD Vision. Projects between Vaults allows groups collaborating across several vaults to search and visualize their data side-by-side in a single view. CDD Vision is enhanced with multiple scatter-plots.
New White Paper: Promoting Effective Project Teams for Drug DiscoveryAugust 6, 2015-Meeting the Informatics Needs of All Team Members When only 1 in 10 drugs tested in humans gets to the market, and those take 10-12 years to go through the process, it’s amazing when any drug discovery and development team is successful! A new white paper is available which explores the mechanisms for meeting the [...]
CDD CEO Barry Bunin Featured in SLAS ELN InterviewJuly 20, 2015-Before The Cloud was a regular part of our lexicon, entrepreneurs such as Barry Bunin pioneered secure, collaborative data hosting for scientists. “We have all the ideas for a Nobel Prize here in this lab. The problem is that the ideas are in separate brains instead of one. If we could gather everything into one [...]
CDD Hosts Workshop, Presents Papers and Posters at the 250th ACS National Meeting & Exposition in August 2015July 16, 2015-CDD hosts CDD Vision Workshop while Dr. Sean Ekins (CDD’s Chief Scientific Officer) presents papers and posters at the 250th ACS National Meeting & Exposition in August 2015 Dr. Ekins’ presentations will be part of the technical program at the 250th ACS National Meeting that will be held in Boston, MA. YOU are Invited to [...]
Rapid prototyping From TB Mobile to CDD ModelsJuly 8, 2015-Rapid prototyping From TB Mobile to CDD Models From the desk of CDD CSO Sean Ekins, M.Sc., Ph.D., D.Sc. If I have seen further it is by standing on ye sholders of Giants – Isaac Newton As someone working in drug discovery you cannot escape what appears to be the vast number of papers (and [...]
Some Clouds Are Lined With Silver, Some Are Lined With GoldJuly 1, 2015-As a research scientist in the health field, concerned with hastening the pace of therapeutic advances, my pulse quickens at the thought of clouds laden with research data, coalescing into a storm of Eureka moments. I imagine new collaborations and alliances producing a rain of ideas and hypotheses to quench the drought of therapies for the many ills that plague our bodies.
While Google and Apple wrestle over who will siphon the most data into their private storehouses, other companies and organizations have established and promoted the Cloud as a conduit for collective gains, offering the vision and potential for a Cloud lined with gold....
Machine Learning Models and Pathway Genome Data Base for Trypanosoma cruzi Drug Discovery published in PLOS Neglected Tropical DiseasesJune 26, 2015-We are pleased to announce that the results of a phase I STTR collaborative study on Chagas Disease with groups at SRI International, UCSD, and UCSF have just been published in PLOS Neglected Tropical Diseases.
Chagas disease is a neglected tropical disease caused by the eukaryotic parasite Trypanosoma cruzi. We used a combination of cheminformatics, bioinformatics, in vitro and in vivo testing to identify molecules active at eliminating the parasites from infected cells. We found that the European Medicines Agency approved antimalarial drug pyronaridine possessed 85.2% efficacy (reduction in parasite burden compared to untreated control group after 4 days treatment) in the acute Chagas mouse model and may represent a repurposing opportunity.
This study also utilized the public T. cruzi datasets present in the CDD Vault. “This project demonstrates what can be achieved by combining complimentary approaches...
CDD Awarded $1.5 Million Grant to Simplify Encoding of Bioassays with Automated Annotation TechnologyJune 17, 2015-Burlingame, Calif.—June 17, 2015—Collaborative Drug Discovery, provider of CDD Vault® web-based drug discovery informatics platform, announced they have been awarded a $1.5M Phase 2 SBIR grant to use the Bioassay Ontology Annotator as the foundation for a collaborative CDD ELN (Electronic Laboratory Notebook).
The Bioassay Ontology Annotator software provided a strong proof-of-concept that one could use new automation technologies for comparison of assay conditions
CDD Vision Update: Launching Vision nowMay 2, 2015-We’re thrilled to announce the inaugural release of CDD Vision. Fully integrated with CDD Vault, CDD Vision provides powerful and intuitive visual analysis and plotting features. Whether you are a biologist looking for selective compounds, or a medicinal chemist looking to optimize chemical properties of active compounds, CDD Vision provides the tools to analyze and [...]
CDD Presents Papers and Posters at Cambridge Healthtech Institute’s Twelfth Annual Mastering Medicinal Chemistry in June 2015April 29, 2015-Dr. Barry Bunin (CDD's President and CEO) will present papers and defend posters at the 2015 Mastering Medicinal Chemistry in June 2015 at the Westin Waterfront in Boston, MA
Come visit us in Booth 18
CDD will be exhibiting the latest developments in our hosted solution for bioassay data management, chemical registration, and Structure Activity Relationship (SAR) analyses. Please visit us at Booth 18 in the Exhibit Hall between June 10-11, 2015, to witness the power and flexibility of CDD Vault...
On Demand Video from the pIC50 Scientific WebinarApril 15, 2015-CDD’s recent live webinar event about the merits of pIC50 was a great success. To summarize, Dr. Marc Navre endeavored to convince the audience to think logarithmically, and why the use of pIC50 values to share the results of in vitro assays with colleagues is easier, smarter and cleaner than using “old-fashioned” IC50 values. Live examples of using CDD Vault and CDD Vision to enable these calculations were also presented.
If you missed it, or would like to share with your colleagues, you can download the slides or check out the complete presentation...
Collaborative Drug Discovery Books – Part 2March 31, 2015-When we are not writing code, planning strategy, or increasing customer delight here at CDD, we learn from a variety of books covering topics. Here in part two we look deeper within the brain to see what drives us all, how to drive better, and how we can collaboratively synergize given the nature of group dynamics. We'd like to share these five additional books you may find interesting...
Seminar: An Afternoon with Collaborative Drug DiscoveryMarch 25, 2015-An Afternoon with Collaborative Drug Discovery
Monday, April 27th
1:00 - 4:00 pm ET
Come be a part of our free seminar to hear how local researchers are applying research informatics to their chemical and biological experiments. Learn about chemical registration, data archival, data analysis, database enhanced collaborations and how to create a data model that allows you to leverage all these components within your research project. We will use the intuitive, user-friendly CDD Vault drug research informatics platform. Hands-on experience will be provided for those interested...
Webinar: Why Using pIC50 Instead of IC50 Will Change Your LifeMarch 17, 2015-Why Using pIC50 Instead of IC50 Will Change Your Life
Marc Navre, Ph.D.
20-Minute Online Webinar: Wed, April 15th at 2pm ET, 11am PT
In a brief but entertaining webinar, Dr. Navre will convince you why the use of pIC50 values to share the results of in vitro assays with your colleagues is easier, smarter and cleaner than using “old-fashioned” IC50 values. A 25-year veteran of the industry, Dr. Navre implemented this change in three biotech companies with great success where even the firmest opponents became believers. See how using pIC50 values and thinking logarithmically helps you design better experiments, gives you a better sense of the relative potencies of compounds, and how you and your colleagues...
Collaborative Drug Discovery BooksMarch 16, 2015-When we are not writing code, planning strategy, or increasing customer delight here at CDD, we seek enrichment from a variety of books covering topics from drug discovery to discovery at large. Discovery as the quest for novelty, is one the great motivators for all researchers. And insights come from some unlikely sources, like from the "theater" of the emergency room or the lessons of persistence leading to the first antibiotic.
We'd like to share with some books you may find of interest:
The Demon in the Microscope...
CDD To Attend the 2015 Bio-IT World Conference & Expo in April 2015March 9, 2015-CDD will attend and exhibit at the 2015 Bio-IT World Conference & Expo in April 2015 at the Seaport World Trade Center in Boston, MA
Come visit us in Booth 152
CDD will be exhibiting the latest developments in our hosted solution for bioassay data management, chemical registration, and Structure Activity Relationship (SAR) analyses. Please visit us at Booth 152 in the Exhibit Hall between April 21st and April 23rd, 2015...
Databases and collaboration require standards for human stem cell researchFebruary 20, 2015-Last year CDD has published a review about databases and collaboration in the area of human stem cell research. The article is now published in Drug Discovery Today * and you can get a free copy for the next month or so. The goal of the article was to examine the current public data space in stem cell research, and to find the gaps. We also provide an example of how the CDD Vault can be used to solve the main problems of secure data sharing...
CDD Vision Update: More Calculations with Protocol ConditionsFebruary 14, 2015-This release adds new features to protocol conditions and dose-response calculations. In summary, you can now specify multiple condition values in your custom formulas, your search results will now show a separate column for each protocol condition, and you have more flexibility when defining dose-response curve validation.
CDD chairs sessions, presents papers and defends posters at 22nd International Molecular Medicine Tri-Conference in February 2015February 7, 2015-Dr. Barry Bunin (CDD's President and CEO) will present papers, defend posters and chair sessions at the 22nd International Molecular Medicine Tri-Conference in February 2015 at the Moscone North Convention Center in San Francisco, CA
Come visit CDD in Booth 3
CDD will be exhibiting the latest developments in our hosted solution for bioassay data management, chemical registration, and Structure Activity Relationship (SAR) analyses. Please visit us at Booth 3 in the Exhibit Hall between February 16th and 18th, 2015, to witness the power and flexibility of CDD Vault.
Accelerated Drug Discovery Perspectives Given the Ebola Virus OutbreakFebruary 3, 2015-Like many around the world, we have been watching the devastating effects of the Ebola Virus in West Africa. We have been impressed by the important contributions of the health organizations and medical workers that have served patients at great personal risk to themselves and brought the disease under some degree of control. Especially during a crisis, seamless effective collaborations are critical. Collaboration can catalyze the communication of current knowledge and coordinate future action – whether for drug repurposing or de novo drug discovery. We wondered, how can those of us in drug discovery contribute in some way? We have found considerable interesting published results regarding molecules showing some activity against the Ebola Virus, including a number of FDA-approved drugs and made them available as a public data set in CDD Vault for the scientific community.
CDD Vault for medicinal chemistry decision support in large collaborationsJanuary 21, 2015-Last week I attended the More Medicines for Tuberculosis (MM4TB) consortium meeting in Bilbao Spain. The MM4TB consortium consists of over twenty partners from thirteen countries in Europe, America, Asia and Africa. This event happens twice a year and represents an opportunity to bring the various groups together to discuss scientific progress. The meetings are also a chance to socialize with colleagues and share TB experiences and insights over two full days of work and leisurely lunches and dinners.
CDD to Present at SLAS Meeting in FebruaryJanuary 12, 2015-CDD will be presenting two scientific talks at the upcoming Society for Laboratory Automation and Screening (SLAS) Conference in Washington, DC, between February 7th and 11th, 2015. Dr. Barry Bunin, CEO of CDD, will be chairing one of the Informatics sessions and presenting a talk entitled “10 Years Securely Hosting Collaborative Drug Discovery CDD Vault [...]
Beware Researchers! Challenges Navigating Commercial and Public DatabasesDecember 16, 2014-From the desk of CDD CSO Sean Ekins, M.Sc., Ph.D., D.Sc. Each of the phases of a drug discovery project is directly impacted by the quality and availability of relevant data. There is no question that well-curated chemical structures and linked bioactivity data enable drug discovery projects. This is true whether managing a single organization, sharing [...]
CDD Vision Update: Calculations with Protocol ConditionsDecember 13, 2014-The full power of recently introduced protocol conditions is realized with this release, incorporating conditions into CDD Vision calculations. This means your data entry and management is simplified with fewer protocols, and data processing and analysis is flexible and powerful using conditions.
It’s all about the data, ‘bout the data, no trouble – CDD Holiday PoemDecember 5, 2014-The holiday season is a time of retrospection and merriment. At CDD, we have a tradition of a sharing a holiday poem (See 2013, 2012, 2011, etc.). This year, we’ve been a bit more playful and have written this year’s poem to the catchy tune of Meghan Trainor’s “All About That Bass” which has been [...]
CDD Vault Update: Averaging numbers with modifiersNovember 26, 2014-In this update, we have changed the way numbers with numeric modifiers, such as IC50 values, are averaged. Previously imported data were automatically recalculated following the new rules, which are better suited to drug discovery applications.
Whoa! Our Customers Are Just The Best!November 20, 2014-These lighthearted videos from the Martin Research Group at the University of Texas just made our day! We at CDD laughed until we cried with appreciation of all the creative work those guys and gals put into producing these awesome videos. We appreciate the subtle humor and are grateful for their creative way of sharing the “happy CDD Vault user” experience.
Let us know which scene is your favorite...
Machine Learning from an Expert’s Evaluation of Compounds November 14, 2014-CDD has recently developed, as part of CDD Vision, the ability to build machine learning models. These can be used to make predictions for properties of molecules that may not have been tested. Once a scientist chooses a “good” set of compounds, perhaps with a desired bioactivity, and a “bad” set, the inactives, with a single [...]
CDD Joins Ryoka at the 32nd Medicinal Chemistry Symposium in Kobe, Japan, on November 26-28, 2014November 13, 2014-CDD joins our Japanese distributor, Ryoka Systems, at the 32nd Medicinal Chemistry Symposium event in Kobe, Japan, on November 26-28, 2014 CDD, along with Ryoka Systems, will be attending and presenting at the 32nd Medicinal Chemistry Symposium (MCS2014), which will be held at the Kobe International Conference Center in Kobe, Japan, between November 26th and [...]
CDD’s CSO is scheduled to speak and present a poster at the In Silico Drug Discovery Conference in December 2014November 11, 2014-Dr. Sean Ekins (CDD's Chief Scientific Officer) is scheduled to speak and present a poster at the In Silico Drug Discovery Conference in December 2014
The In Silico Drug Discovery Conference will be held at the Hamner Conference Center in Durham, NC, on December 3rd and 4th, 2014. Dr. Sean Ekins, CSO at CDD, will be presenting a talk and a poster at the In Silico Drug Discovery Conference. The conference is being hosted by the North Carolina Biotechnology Center in the Hamner Conference Center, and is slated to include expert speakers, panelists, researchers, and product vendors.
CDD Launches CDD Advocate ProgramNovember 4, 2014-Announcing CDD Advocate!!
In the spirit of collaboration, CDD is happy to announce the launch of the CDD Advocate program. This program is a network of professionals in the drug discovery research space dedicated to raising the awareness of CDD's very cool and unique technology, CDD Vault. At CDD, we've always understood the power of collaboration. As a progressive web company, we encourage collaborative ventures and are committed to our philosophy that working together is a crucial aspect to success in today's research environment.
Members of our CDD Advocate program will be...
CDD Announces Partnership With Ryoka SystemsNovember 3, 2014-Ryoka Systems becomes CDD Reseller in Japan Collaborative Drug Discovery (CDD) is excited to announce the appointment of Ryoka Systems as the Japanese distributor for CDD Vault. The new partnership makes this flagship platform broadly available with local support and customized training for researchers in Japan. CDD Vault is widely used for Structure-Activity (SAR) analysis, [...]
CDD Vault Update: Maximum Measured ActivityNovember 3, 2014-Concentration response calculations- minimum and maximum measured activity are now reported.
API addition- download readout rows by run ID instead of run date. CDD Vision gets an update: you can build a predictive model from a molecule collection. And the release notes move to the CDD blog.
CDD to Attend the 3rd Annual Conference of the International Chemical Biology Society (ICBS) in San Francisco in November 2014November 1, 2014-CDD will be attending the 3rd Annual Conference of the International Chemical Biology Society (ICBS) in San Francisco between between November 17th and 19th, 2014. Personal demonstrations are available at Booth TT-12 during the ICBS Conference! Visit us to witness first-hand the power and flexibility of CDD Vault, which combines a bioassay database and chemical [...]
In Case You Missed It, Check Out The Video From CDD’s Recent Scientific WebinarOctober 29, 2014-CDD’s recent live webinar event was a great success. To summarize, first, Dr. Chris Lipinski, reknowned medicinal chemist and CDD Scientific Advisory Board member, described the importance of considering enthalpy and entropy when optimizing for ligand affinity, and how this might differ between drug discovery techniques. Using the custom calculations available in CDD Vision, we defined [...]
CDD Spotlight Interview with Thale Jarvis, Crestone Inc.October 23, 2014-"People sometimes refer to it as drug hunting. It starts with early discovery, finding interesting compound libraries and screening for hits, followed by a lot of intensive medicinal chemistry, microbiological and biochemical characterization and preclinical testing. Once you have an IND candidate, the focus expands to include process chemistry and toxicology testing. And that’s before you even consider human clinical trials. It’s a long process, but terrifically engaging. You have to balance optimism with realism. It takes great teamwork; to succeed, your team has to be smart, tenacious and lucky in about equal measures."
Get Ready for CDD’s First Live Webinar Event!October 14, 2014-In preparation for our webinar next week, we at CDD have been busy investigating trends across CDD Public datasets. With data on more than two million compounds and unlimited capability for generating custom calculations, there has been no shortage of intriguing findings. For example, when experienced medicinal chemist Chris Lipinski suggested that there may be [...]
CDD Vault Update: Improved Structure EditorOctober 11, 2014-The Javascript-based structure editor we introduced earlier this year is great, but it was missing a few key features, such as support for direct copy and paste of structures. We are happy to report that this update should address the most common requests.
CDD Vault Donation for Ebola ResearchersOctober 9, 2014-In Western Africa, Ebola has already killed more than two thousand people, and the Center for Disease Control (CDC) has estimated up to 1.4 million people could contract the deadly virus in the coming months in a worst-case scenario. Despite the growing threat, there is still no therapy that can be distributed at a large-scale. [...]
A novel collaborative, fast-paced workflow: From a discussion on Twitter to a micropublication on EbolaOctober 3, 2014-From the desk of CDD CSO Sean Ekins, M.Sc., Ph.D., D.Sc. We are all aware of the nightmare going on in Africa, and now elsewhere, regarding the spread of the Ebola virus. Although it is important to point out so far it has killed a small fraction of the hundreds of thousands that have likely [...]
CDD Vault Update: Introducing Protocol ConditionsSeptember 26, 2014-You can now indicate that a readout definition is a protocol condition. Designating a readout definition as condition may not appear to be an exciting feature, but this release could revolutionize how you manage and process your assay results. Imagine that you run the same assay with five different species, and you want to see an average value for each molecule.
A Conversation on Drug Discovery BiasesSeptember 18, 2014-From the desk of Chris Lipinski, PhD I’ve been thinking a lot lately about how to optimize for ligand affinity. Of course, this is a central theme of all drug discovery projects. At its core is the question of how physical and chemical relationships guide the interplay between the ligand, the protein target, and the [...]
Announcing CDD’s First Live Webinar Event – Are Your Compounds Biased by Your Discovery Techniques? September 8, 2014-Entropic and Enthalpic Propensities Inherent in SBDD and HTS. Dr. Christopher Lipinski Dr. Matthew Soellner Dr. Barry Bunin Online Webinar: Wed, Oct 22 from 2-3pm ET Christopher Lipinski’s decades of experience practicing medicinal chemistry for Pfizer and post-Pfizer have led him to believe that there are inherent biases in the molecules developed via different drug discovery [...]
CDD Innovation: A New Tool for Annotating BioassaysSeptember 2, 2014-CDD’s informatics research wing has been busy this summer. In a collaboration with the Bioassay Ontology Project at the University of Miami and funded by a NIH SBIR Phase I grant, CDD has prototyped a new tool for annotating bioassay data. Our method is fully described in this paper, just published in PeerJ: Fast and accurate semantic [...]
Collaboration in the Twitter AgeAugust 28, 2014-From the desk of CDD CSO Sean Ekins, M.Sc., Ph.D., D.Sc.
Scientific conferences can be huge ungainly affairs with tens of thousands of attendees spread over many concurrent sessions and possibly locations. These meetings are great for networking but it is likely any single attendee will only be exposed to the smallest fraction of the science being presented. How could anyone imagine capturing all the data or even a fraction of it presented orally let alone the content of the posters? Being unaware of the science may not be optimal in finding potential collaborators either. Good examples for chemists include...
CDD Vault Update: Image Sizes and Solvents of CrystallizationAugust 20, 2014-Adjustable image size in the search results table “Small” molecules come in a variety of sizes, and you can now adjust the structure images to suit your molecules and eyesight. Dose-response plots and images from uploaded files also scale to the same small, medium, or large previews in the search results table. The size is [...]
Collaboration Paves the Road for Ebola TreatmentAugust 19, 2014-In the throws of the largest Ebola outbreak ever, with more than 2000 confirmed cases in West Africa, there was a glimmer of hope when the little known biotechnology company Mapp Biopharmaceuticals gave their potentially life-saving drug, ZMapp, to two infected patients. ZMapp has very encouraging results in non-human primate studies, but has not been tested [...]
Making the NIH Chemical Probes (over half a billion dollars of NIH investment) accessible in CDD PublicAugust 15, 2014-The Molecular Libraries Program (MLP) has been a tremendous resource for academic labs to pursue the development of chemical probes in a wide range of biological processes. The National Institutes of Health (NIH) has funded extensive HTS efforts, by conservative estimates over half a billion dollars has gone into the program, and we wanted to [...]
CDD Spotlight Interview with Dale Cameron, viDA Therapeutics Inc.July 28, 2014-"It was the first time in my career that I can remember, where creativity and outside the box thinking allowed for mixing and matching a lot of different and unrelated tools, to do something they weren’t originally intended, to generate a result that had immediate and positive effect on our research programs. Completely unpublishable work, I must admit, but...our own crystal structures would eventually come sometime later in the program, and when compared to our hand-made model of a model, we were very close, to the point where the crystal structure simply validated our model, which for a computational chemist, was intensely satisfying."
CDD Vault Highlighted in Scientific Computing ArticleJuly 24, 2014-In the June 2014 issue of Scientific Computing, industry expert Michael Elliott heralds the emergence of robust cloud technologies to support research virtualization. “Collaborative Drug Discovery is the most mature of the group,” he points out, and we are flattered that he has noticed our pioneering position. He goes on to point out that new [...]
CDD Vault Update: Search Results and Z-ScoreJuly 19, 2014-Full width search result table The search results table now uses the entire width of your screen, maximizing the data you can see without needing to scroll. Structure search limit The maximum number of structures matched by a similarity or substructure search has been increased to 100,000. A clear message is now shown when this [...]
Why using pIC50 instead of IC50 will change your lifeJuly 14, 2014-A significant number of CDD Vault subscribers use IC50 values to store and analyze their dose response data from in-vitro assays. Now that the automated calculations extension of CDD Vision supports the calculation of pCI50 values, I’d like to convince users of IC50 to consider using pIC50 instead, and why it will make your life easier (in the long run), and just make you a finer human being.
Drug Discovery in the Age of the Customizable Genome: Implications of the CRISPR RevolutionJuly 8, 2014-The CRISPR/Cas9 system allows for unprecedented ease and access to editing the genome, offering drug discovery researchers creative and precise control when designing and developing screening assays. Application of CRISPR/Cas9 has spurred collaborations, led to key advances in diverse fields from neglected and rare diseases to cancer and gene therapy, and has the potential to shift the landscape of drug discovery.
CDD Vault Update: Calculations Using Multiple ProtocolsJune 28, 2014-The flagship feature of this release is the ability to perform calculations using results from multiple assays. This allows you to calculate the selectivity index and similar metrics. Calculations between protocols – part of CDD Vision The readout definitions you use in calculations can now come from multiple protocols. Like all calculations in CDD Vision, [...]
CDD’s Public Database is a Valuable ResourceJune 24, 2014-CDD Public offers CDD Vault users access to more than 100 well-curated datasets that can be easily mined and analyzed in conjunction with your own private data. Compounds stored in CDD Public can be easily searched and filtered using the CDD Vault‘s easy-to-use, chemically intelligent interface. In addition, CDD has recently developed the ability to [...]
Introducing Eight New Chemical Libraries in CDD VaultJune 24, 2014-BURLINGAME, Calif. and Niagara-on-the-Lake, Canada — June 24, 2014 — Collaborative Drug Discovery (CDD) and Life Chemicals are proud to announce the availability of eight new chemical libraries in the CDD Vault software platform. These collections have over 370,000 original compounds selected for diversity and lead-like or drug-like properties. “We decided to highlight some of the [...]
CDD to Attend Enabling Future Pharma Conference in July 2014June 12, 2014-CDD will be attending the Enabling Future Pharma: Strategic Initiatives in Collaborative Innovation in Drug Discovery, Heralding the Mutually Inclusive Role of NIH, Academia, Pharma and Patient-Based Organizations Conference in Chicago between July 9th and 12th, 2014.
CDD’s CEO, Dr. Barry Bunin, is scheduled to present a talk in the "Cutting Edge Research-Tools, Technologies for Chemical Biology" track at 5:00 pm on Friday, July 11.
Dr. Bunin's presentation is titled “The Collaborative Drug Discovery Paradigm: Modern Drug Research Informatics Applied to CNS, Infectious, Neglected, Rare and Commercial Disease Applications”....
WIIFY Part 3 – Modern Drug Discovery Tools for Large Collaborative ConsortiaJune 11, 2014-A three part series exploring the unique challenges of Consortia scientists
Part 3 – What’s in it for you, the person who actually has to do the work
You are the one actually doing the work, the hard work that others eschew. Parts of science can feel like working in quicksand, with handcuffs on. There are multiple problems, and as soon as you fix a problem, new ones emerge. You must do reproducible science - the hallmark of good science. On top of all the experimental challenges, you have this mountain of data to deal with. Big data typically means big headaches. And whose lap does all this data fall into – why yours, of course. As if you are not busy enough? Isn’t it enough to just run all these experiments? Who has time to look at thousands or even millions of data points? Even worse than the numbers are the formats, the raw data from the plate readers or other instruments is different than the format needed to make heads or tails of the data relative to the controls you painstakingly included in the appropriate columns. When something unexpected happens (and when doesn’t that happen) like an instrument hiccup, or running out of a key reagent midway through a run, then the data must be looked at within the context of whatever the unexpected anomaly happens to be this time. Yes big data = big headaches. Well fret no more, you have a partner by your side each step of the way with CDD.
CDD has felt your pain and is your ally in the fight for your right to generate understandable, reproducible, and manageable data. Wasn’t that in the constitution somewhere?
Collaborative Drug Discovery (CDD) Announces Customer Advisory Board (CAB) MembersMay 27, 2014-BURLINGAME, Calif. — May 27, 2014 — Collaborative Drug Discovery (CDD) is delighted to announce the members of our commercial Customer Advisory Board (CAB). The following industry thought leaders were carefully selected to help guide the short-term and long-term development of the CDD Vault platform:
Jeff Blaney, Director Computational Chemistry & Chemoinformatics (Genentech)
Henry Johnson, Senior Scientist (Amgen, Onyx Pharmaceuticals subsidiary)
Thale Jarvis, VP Research & Development (Crestone Pharmaceuticals)
Mark Gurney, CEO (Tetra Discovery Partners)
Paul Humphries, VP Chemical Sciences (Reset Therapuetics)
Daniel Erlanson, President (Carmot Therapeutics)
As reported at the 10 Year Anniversary CDD User & Community Meeting, CDD Vault has the same number of user logins/month as a full year in 2008.
CDD’s Product Manager, Kellan Gregory, commented...
CDD Vault Update: Calculations and ModelsMay 10, 2014-We introduce CDD Vision, a new analysis and visualization product, predictive model building within CDD Vault, and a half-dozen smaller enhancements. We are excited to see what you can achieve with the tools in this release. Calculations within a protocol – part of CDD Vision This is the introductory release of CDD Vision, an optional [...]
Open source ECFP/FCFP circular fingerprints in CDKMay 10, 2014-CDD Vault now allows you to build predictive models. Because we believe in collaboration and reproducible results, we are releasing the core algorithms that underly this feature as open source software. The chemical fingerprints are detailed below, and we have also released our modified Bayesian model. Send an email to info@collaborativedrug.com if you’d like to try using [...]
CDD Spotlight Interview with Enrique Michelotti, NIMH/NIHMay 7, 2014- "I think the biggest impact was people in academia that were not used to databases and with the training and the use, they came to realize how powerful it is to have a permanent central repository, where you can access the data very fast and correlate the most salient patterns. I think that is the most important impact by providing this new capability that was even useful for people that were just not used to databases. It really speaks to the ease of use and overall design of CDD Vault."
CDD Spotlight Interview with Paul Humphries, Reset TherapeuticsApril 17, 2014-"As a company we all have to have a phenotypic drug discovery mindset, which means that we have to be prepared for any target (or working on an unknown target) that acts through any compartment (liver, CNS, etc) that modulates physiological endpoints for any disease. I’m no longer a target-based medicinal chemist working on metabolic diseases, I’m a phenotypic drug discovery scientist working on circadian modulators that are disease agnostic. It’s an exciting, challenging and hugely rewarding part of my career and I am relishing working with the Reset team to create a new path for drug discovery in this novel scientific area."
Part 2: CDD’s Tenth Anniversary Meeting HighlightsApril 14, 2014-On Friday April 4th, CDD celebrated its tenth anniversary by hosting a community meeting at UCSF. We have written about the meeting before, but there is so much more to share that wasn’t covered. For starters, new CDD Vault tools were presented at the meeting, including calculations for the new CDD Vision module and QSAR models. [...]
Part 1: CDD’s Tenth Anniversary Meeting HighlightsApril 9, 2014-On Friday April 4th, CDD celebrated its tenth anniversary by hosting a community meeting at UCSF. From all of us at CDD, we want to give a great big “Thank you!” to everyone who participated. We appreciate all those who prioritized their time out to fly/drive/walk to the conference, to present, to sponsor the event, to participate in panels, to listen attentively, and to ask questions. WOW!
CDD to attend Drug Discovery Chemistry Conference in San Diego in April 2014April 7, 2014-CDD will be attending the Drug Discovery Chemistry Conference in San Diego between April 23rd & 25th, 2014. CDD’s Scientific Relations Consultant, Dr. Adam Kallel, is scheduled to present a poster at the Drug Discovery Chemistry Conference in San Diego between April 23rd & 25th. Dr. Kallel’s poster is titled “Leveraging CDD Vault®’s Kinome Data [...]
Reflections on World TB DayMarch 24, 2014-My maternal grandfather died of tuberculosis. He contracted it while serving in the First World War. He returned from France to live a life of diminished quality, shortened by an early death. I can also remember, when I was a small child, in the 1970’s going for rides through Los Angeles’ Elysian Park area and passing what was then the Barlow Sanatorium. I asked my dad what a sanatorium was and was introduced at a young age to, what was still then, the isolating treatment of tuberculosis. The Barlow Sanatorium is now the Barlow Respiratory Hospital. Los Angeles, fortunately, no longer has the need for a facility dedicated to the treatment of TB.
CDD’s 10th Anniversary Community Meeting Agenda Now OnlineMarch 20, 2014-If you haven’t already heard, we are celebrating our “10 Years of Collaborative Drug Discovery” by hosting a CDD user and community meeting at the UCSF Mission Bay conference center in San Francisco on Friday, April 4th. We have assembled an exciting day of presentations, panels, and discussion groups you can now see online (Agenda). [...]
CDD to attend Mastering Medicinal Chemistry Conference in May 2014March 14, 2014-CDD will be attending the 11th Annual Mastering Medicinal Chemistry Conference in Boston on May 21st and 22nd, 2014. CDD’s CEO, Dr. Barry Bunin, is scheduled to present a talk in the “Case Studies Session: Part III” track at 11:05 am on Thursday, May 22. Dr. Bunin’s presentation is titled “Modern Drug Research Informatics Applications [...]
CDD Vault Update: Averages and NormalizationMarch 14, 2014-Readout definitions: more flexible averaging You can now choose a different level of aggregation for each average readout, whereas previously the aggregation level was uniformly set for all readout definitions in the vault. The available aggregation levels are as follows: Batch/Run is good for replicate data in a single experiment (run). Replicated data from the [...]
Remembering Dr. ZaffaroniMarch 8, 2014-When I first became an entrepreneur the one person whom I especially wanted to work with was Dr. Alejandro Zaffaroni. I was blessed to have some unique experiences working with him that I thought would be worth sharing. As many of you know, Dr. Zaffaroni was involved in fundamental biotech innovations ranging from the birth control pill to the patch to the Affymetrix gene chip. Generally he'd be involved on the technical, business, and people sides. On March 1 2014, at age 91, Dr. Zaffaroni passed away. His inventions of course impact many lives, yet how he worked directly with people was equally compelling. Mario Rosati once mentioned to me that Dr. Zaffaroni was the best he had seen in a board room. I thought I would share a few personal stories from my own interactions with him that have stuck with me over the years.
KeytoLead AB and CDD, Inc. would like to invite you to their joint seminarMarch 6, 2014-KeytoLead AB and CDD, Inc. would like to invite you to their joint seminar: Medicinal Chemistry and Data Management in Modern Drug Discovery 27th March 2014, 14:00‐16:30 Apotekarsocietetens bibliotek, Wallingatan 26A, Stockholm Through clever medicinal chemistry, KeytoLead advances drug discovery targets into high‐quality starting points tailored for the pharmaceutical industries’ pipelines. KeytoLead manages entire lead [...]
WIIFY Part 2 – Modern Drug Discovery Tools for Large Collaborative ConsortiaMarch 5, 2014-A three part series exploring the unique challenges of Consortia scientists Part 2 – What’s in it for you, the Lead Scientist funded by an external source You love science. That is why you became a scientist. You are good at it. You like being part of the scientific conversation mirrored in the literature and [...]
CDD Vault Update: Preventing DuplicatesFebruary 28, 2014-This release makes it easier for you to avoid registering duplicate structures and includes a collection of other enhancements. Tautomeric structure detection When new structures are registered in the CDD Vault, they are compared to existing molecules. If equivalent structures are found by InChIKey, a suspicious “unintentional duplicates” event is reported. When this event is [...]
WIIFY Part 1 – Modern Drug Discovery Tools for Large Collaborative ConsortiaFebruary 25, 2014-A three part series exploring the unique challenges of Consortia scientists Part 1 – What’s in it for you, the person ultimately responsible for extracting value from a collaborative mixture of heterogeneous academic, CROs, and drug discovery brains. You have been successful in your career. And your reward is the enormous responsibility of advancing a [...]
CDD’s CEO & CSO to present papers and chair sessions at 247th ACS National Meeting & Exposition in March 2014February 13, 2014-Dr. Barry Bunin (CDD’s President and CEO) and Sean Ekins (CDD’s Chief Scientific Officer) will present papers and chair sessions at the 247th ACS National Meeting & Exposition in March 2014 These presentations will be part of the technical program at the 247th ACS National Meeting that will be held in Dallas, Texas. Podium [...]
WIIFY Part 3 – Modern Drug Discovery Tools for ex-Pharma ScientistsFebruary 11, 2014-A four part series exploring the unique challenges of ex-pharma scientists Part 3 – What’s in it for you, the pure scientist? You were attracted to science because of the purity of the pursuit. You saw the opportunity to examine nature as it is, as objectively as possible. You saw a way to do some [...]
WIIFY Part 2 – Modern Drug Discovery Tools for ex-Pharma ScientistsFebruary 4, 2014-A four part series exploring the unique challenges of ex-pharma scientists Part 2 – What’s in it for you, the manager of the group, the person on the hook if the project succeeds or fails? Whether you have a small group handling all experiments internally, or a distributed team spanning the globe, you need to [...]
WIIFY Part 1 – Modern Drug Discovery Tools for ex-Pharma ScientistsJanuary 28, 2014-A four part series exploring the unique challenges of ex-pharma scientists Part 1 – What’s in it for ex-pharma scientists who need to make magic happen on a shoestring? You used to work in Big Pharma. So you know what it takes, what it really takes, to generate a rock-solid compound. You’ve seen integrated teams [...]
CDD to attend Molecular Medicine Tri-Conference in February 2014January 27, 2014-CDD will be attending the 21st International Molecular Medicine Tri-Conference in San Francisco between February 9th and 14th, 2014. CDD’s CEO Dr. Barry Bunin is scheduled to chair the “Pre-Competitive Collaboration & Supporting Public-Private Partnerships” track beginning at 2:15 pm on Tuesday, February 11, in the “Integrated R&D Informatics & Knowledge Management” channel. Dr. Bunin [...]
CDD Vault Update: Bigger and Better ChemistryJanuary 24, 2014-We’ve upgraded our chemistry software and replaced the structure editor. The new ChemAxon Marvin Javascript-based structure editor loads faster and won’t break every time there is a Java security update. Snazzy! New structure editor Marvin for JavaScript, the new structure editor, is used throughout the CDD Vault. It loads quickly, is independent of Java, and will [...]
CDD to attend SLAS meeting in January 2014January 3, 2014-CDD will be attending the 3rd annual Conference & Exhibition hosted by the Society for Laboratory Automation and Screening (SLAS) in San Diego between January 20th and 22nd, 2014. CDD’s CSO, Dr. Sean Ekins, will be presenting a talk and a poster at the 3rd Annual Conference & Exhibition hosted by the Society for Laboratory [...]
2013 CDD Holiday Poem – As People We CareDecember 1, 2013-Commercial, neglected disease – Nature indifferent Mechanisms, molecules, methods persistent A molecule is a molecule, a sequence, a sequence A curve is a curve, an equation’s transcendent Money is indifferent, as it well should be But as people we care about malaria and TB And T. brucei, T. cruzi, don’t forget leishmaniasis Which rolls off [...]
A Call to Participate in a Data Sharing Initiative for Neglected Tropical Disease Drug DiscoveryNovember 26, 2013-From the desks of Northeastern Professor Michael Pollastri and CDD CEO Barry Bunin:
Neglected tropical diseases (NTDs) affect over a billion poor people globally. Since there are relatively limited resources to discover new treatments, it is more critical that the those limited resources work optimally together. Efficient collaboration is the key to saving money, time, and to accelerating the drug discovery process.
Since we are already using the CDD Vault for our private collaborations, we are running an experiment with a separate CDD Vault involving selective (secure) sharing with a larger set of Neglected Tropical Disease Researchers. We have made an open call to other NTD labs from around the world to merge their drug discovery data with ours to identify areas of synergy and overlap.
Help Us Build Innovative Products Customers LoveNovember 22, 2013-There’s something very special about working in an environment where your customers truly appreciate the quality and responsiveness of the products you dedicate your working life to build. If you would like to help develop the next generation of informatics systems for collaborative drug discovery research, consider a career with CDD. Dr. Kristina Bender from Stanford recently [...]
CDD Vault Update: Search page updatesNovember 22, 2013-This release brings a collection of handy enhancements to your searches and reports. “Not in” protocol search Have you ever wanted to find molecules that have NOT been tested in an assay so that you can schedule them for testing? With this release we add a “not in protocol” search that allows you to do [...]
Academic drug discovery is not an oxymoronNovember 19, 2013-Last week Northwestern’s Center for Molecular Innovation and Drug Discovery (CMIDD) held it’s 18th annual symposium, which CDD was proud to sponsor. The symposium is geared towards basic research scientists to educate them in the relatively novel academic domain of drug discovery, and to provide the expertise necessary to progress their biological targets through to [...]
CDD Vault Update: New import and search capabilitiesNovember 1, 2013-Update structureless molecules en masse (For vaults that use CDD’s molecular registration system) If you work in a vault with a registration system, you previously had to manually update each structureless molecule when the structure became available. That’s fine for the one-off compound, but a drag for a whole compound library. Now you can bulk [...]
WIIFY Part 5 – Modern Drug Discovery Tools for Startup, Small Biotech, or AcademicsOctober 22, 2013-What’s in it for you as a technician in a budget sensitive startup or academic laboratory, where you are running the experiments, generating the data, and perhaps even maintaining the instruments. Your lab is an intellectual (perhaps self-righteously so) place, but you are the one who actually does the final experiments that generate the screening [...]
CDD Vault Update: Batches can have files tooOctober 11, 2013-The last two releases brought you files-as-readouts. Now you can treat files as a special type of batch field. What does this mean? It means that you can associate images and other files directly with your structures! NMR spectra, MSDS sheets, crystal structures, requisition forms; you get the idea. Vault administrators will need to define [...]
CHARMMing Trio win Nobel Prize in ChemistryOctober 10, 2013-Yesterday Martin Karplus, Michael Levitt and Arieh Warshel won the Nobel Prize in chemistry. Essentially their work has revolutionized computational chemistry and anyone that performs molecular simulations will know of their foundational work well. They basically developed CHARMM.
Much was written about their achievements, some of the press was just vague, claiming importance in many areas from solar cells to drug discovery, but anyone with knowledge of computational science could
Prof. Jonathan Baell of “PAINS” Filters Fame from Monash UniversityOctober 7, 2013-"People are just finding compounds with a bit of activity and really publishing screening hits as though they are genuine optimizable candidates. And these things can be subversive and they can look real, so these publications are kind of getting accepted and unfortunately there's a lot of noise out there, a lot of pollution, and this is one of the things we certainly strive to do here is not to publish something for the sake of publishing, but to publish it after making optimizations showing these are absolutely real."
CDD Vault Update: Do more with your filesSeptember 27, 2013-Bulk file import Last week we debuted files-as-readouts: the ability to attach a file to any experimental result, and view a preview of the file’s contents throughout your CDD Vault. But what if you have 10,000 files you’d like to store? Here’s how: multiple files can now be attached during a single import by uploading [...]
Interview with Jill WoodSeptember 27, 2013-We think that out of the 4 types of Sanfilippo, type D is in the best position for an effective treatment. Type D is also a relatively mild form of the disease compared to Types A, B and C. It is hypothesized that with just a small increase in enzymatic activity, the disease could be drastically improved. A mouse model of the disease and a better understanding of the brain pathology of the disease, will assist us in developing a treatment. It is JJB’s aim to champion Type D research (alongside that of Type C), using our consortium of investigators to test treatments that we are already funding for type C and translate them and test them for type D. We recently learned that we were successful and had won the KO mouse development prize! The press release came out from Taconic who will kindly develop the mouse and donate it to us.
We actually submitted two proposals and we won part of what we had requested to help support our collaborations to find small molecule treatments for Type C. The judges awarded us the CDD Vault prize, so we are looking forward to putting that into action with our scientists and getting them to share their results securely!!
CDD Vault Update: A picture is worth a thousand … data points?September 20, 2013-In the informatics world, a picture may be worth a thousand numbers that you don’t have to enter. Just attach your image, plot, graph, or file and view it right next to your numeric assay results. In this release we introduce the ability to attach files to protocol readout rows so that image previews and [...]
WIIFY Part 4- Modern Drug Discovery Tools for Startup, Small Biotech, or AcademicsSeptember 17, 2013-WIIFY – for the Collaborative Scientist: The CDD Vault technology facilitates real collaboration around data and people. The instant you or others see important trends for an interesting hit series, you can save a search with specific criteria to automatically detect future trends. You can ask better questions and you get better answers. As experiments [...]
CDD to attend ADDC meeting in October 2013September 12, 2013-CDD will be attending the annual Academic Drug Discovery Consortium conference in Nashville from October 9th through 11th, 2013. Come visit us at Booth 20 at the ADDC Exposition to witness the power and flexibility of CDD Vault. The Academic Drug Discovery Consortium was founded in November 2011. Its goal is to create a network [...]
CDD to present at the 7th annual Extremely Large Databases Conference in September 2013September 4, 2013-CDD’s Head of Scientific Informatics, Krishna Dole, will be presenting at the Extremely Large Databases Conference at Stanford University on September 10th, 2013. Krishna’s talk, titled “Scaling the CDD Vault Technology for a Global Community of Drug Discovery Researchers’ Private and Public Use Cases”, will be part of the Lightning Talks session starting at 3:00 [...]
CDD Vault Update: Dose-Response ExtraordinaireAugust 30, 2013-This release brings many sought-after enhancements for dose-response curve fitting, such as overriding IC50s and constraining fit parameters for individual curves. Plus much more; keep reading to find out! Amidst all of these features for biologists, we’ve added one new feature for chemists especially: preserving molecule orientation as drawn. For chemists Preserve molecule orientation and [...]
CDD to present at Drug Discovery Re-Invented conference in October 2013August 26, 2013-CDD’s CEO & President, Dr. Barry Bunin, will be presenting at the Drug Discovery Re-Invented, Emerging Role of Biotechs, Academics and Non-Profits meeting in Arizona from October 16th through 19th, 2013. Barry’s talk, titled “Collaborative Drug Discovery Technology Neglected, Infectious, CNS, and Repositioning Applications”, will be at Noon on October 17th.
CDD at The Science and Tech Forum Sept 28th in Los AngelesAugust 20, 2013-Join CDD’s CEO & President, Dr. Barry Bunin, at The Science and Tech Forum: Los Angeles as he discusses modern drug research informatics applications to CNS, infectious, neglected, rare, and commercial diseases. This forum looks to the future of scientific research by focusing on the tools of 21st Century communication and how they are changing [...]
Dr. Robert Volkmann, Vice President of Chemistry – Mnemosyne & SystaMedicAugust 15, 2013-"What you've done is you've designed a product that works for people like me. It not only works great for me but also works great for our biologists and our CRO chemists in India. ... I just take it for granted that CDD Vault will work and it will work as planned. So I guess for me the test for the value of something is that you can use it without ever thinking about it."
From Mosquito Bite to MalariaAugust 8, 2013-It’s well known that mosquitoes spread malaria, but have you ever seen exactly how mosquitos manage it? One group at the Institute Pasteur that is studying malaria has captured amazing intravital video microscopy of mosquitoes searching for blood vessels inside the host’s skin. The mosquito’s mouth parts are not the single needle that we perceive, but [...]
WIIFY Part 3 – Modern Drug Discovery Tools for Startup, Small Biotech, or AcademicsAugust 8, 2013-What’s in it for you as a scientist – you have many demands on your time. You want to do science and you find yourself spending 90% of your time putting out fires and explaining to others what you already know. And chasing the almighty Dollar, Euro, Yen or Rupee with grants, grant, grants or [...]
Science in the 21st Century!August 5, 2013-Welcome to Science in the 21st Century! Less Time – Less Money – Less Staff – More Complexity – Bigger Problems – Trickier Solutions – Fewer Funding Sources – Tighter Deadlines… The solution to this litany of concerns is also the new paradigm for science – the distributed future – a world where collaboration rules and [...]
5th CDD Users and Community meeting – Registration open!July 30, 2013-To celebrate our “10 Years of Collaborative Drug Discovery” we will host our CDD users and community meeting at the UCSF Mission Bay conference center in San Francisco on April 4th, 2014.
WIIFY Part 2 – Modern Drug Discovery Tools for Startup, Small Biotech, or AcademicsJuly 23, 2013-What’s in it for you as the lab manager – the one ultimately responsible for results and funding? All it takes is one paradigm-shifting experiment or compound to validate your whole approach. You have an interesting hypothesis that’s why you are raising all the money and doing all these experiments. You have a hunch this [...]
CDD Vault Update: Search from a ListJuly 19, 2013-This release allows you to search using a list of molecule keywords, without needing to provide any boolean operators. This means that you can copy-and-paste a list of molecule IDs, batch external IDs, or any other keywords directly from Excel, Word, Notepad or another application. As long as each term appears on a separate row, [...]
Orphagen CEO Scott Thacher, Ph.D. + Director of Chemistry Ruo Steensma, Ph.D.July 12, 2013-"We had Excel sheets all over the place and data from different projects that were just separated in different folders and after a while," says Dr. Ruo Steensma, "It got to the point that it was just hard to manage. We chose CDD, and we’re really happy with the service and the cost and the way the database is evolving."
GSK Published Kinase Inhibitor Set (PKIS) Now Available in the CDD VaultJuly 8, 2013-There has been a lot of buzz around the GSK Protein Kinase Inhibitor Set (PKIS).
As noted in Derek Lowe’s In the Pipeline blog, “The company has made 367 compounds available to any academic investigator working in the kinase field, as long as they make their results publicly available… So if you're in academia, and interested in kinase pathways, you absolutely need to take a look at this compound set."
CDD in Chemical & Engineering NewsJune 26, 2013-The June 24 Issue of Chemical & Engineering News (C&E News) discussed the benefits of using collaborative software within the drug discovery industry. The article highlighted the need to manage and share data between drug firms and the academic labs and CROs.
Around the all important topic of security, Michael Elliott (CEO at Atrium Research & Consulting) mentioned in the article "I would argue that cloud applications have better protection than most companies have behind their firewalls."
CDD Vault Update: Performance and Easier Report CustomizationJune 21, 2013-We are continuously working to improve the performance of your CDD Vault, although we almost never mention it here. After all, good performance should be something you can expect. We’re going to break that tradition with this release, since it includes a major infrastructure upgrade that we’ve had brewing for quite a while. CDD should [...]
Scott Myers, Ph.D., Director of Drug Discovery – NeurOp, Inc.June 19, 2013-"I recall early on trying to understand what should I do if I’m interested in science, but I’m not interested in medicine so to speak, like, being a medical doctor. And I was reading some descriptions about pharmacology and then I realized that sounded pretty exciting and also fit what I really thought I would like to do. That took me to pharmacy school. And in pharmacy school, I really realized I was more interested in the research and so I went the research path… That was over 20 years ago. And between then and now (when I got this job at NeurOp) NeurOp was really what I always wanted to do. I think this level of the in-vitro pharmacology and evaluating novel molecules has always been my main interest."
CDD to attend ACS meeting in September 2013June 19, 2013-CDD’s CEO & President, Dr. Barry Bunin, will be presenting several talks and posters at the 246th National ACS meeting in Indianapolis from September 8th through 10th, 2013. Come visit us at Booth 1107 at the ACS Exposition between September 8th-10th, 2013, to witness the power and flexibility of CDD Vault. Two Talks: Pistoia Alliance and the emerging HELM standard [...]
WIIFY Part 1- Modern Drug Discovery Tools for Startup, Small Biotech, or AcademicsJune 19, 2013-What’s in it for startups, small biotechs or academic laboratories looking for great drug discovery tools…without the great, big price? When looking for important trends across multiple experiments, you can forget about using multiple excel files. You need to be able to see trends quickly, to wisely prioritize precious compounds, reagents, assays, and resources. You [...]
CDD Vault Update: Gargantuan Summer Update!May 31, 2013-In this colossal release we introduce e-mail alerts, reference compound controls with plot overlays, an improved run summary for quality control, and new site navigation. E-mail Alerts Now you can automatically be notified when new results are added to CDD. These alerts are fully configurable, so you have control over the types of events that [...]
Cheaper and faster screening for antibacterialsMay 8, 2013-BURLINGAME, Calif. — Scientists have collaborated to develop a way to reproducibly find promising molecules against the bacteria tuberculosis (TB) in silico, using off the shelf software. A team led by Sean Ekins at Collaborative Drug Discovery in Burlingame, CA with co-authors at the University of Medicine and Dentistry of New Jersey, Southern Research Institute, [...]
How you move compounds may matterMay 6, 2013-Dispensing Processes Impact Apparent Biological Activity From the desk of Sean Ekins, VP Science, Collaborative Drug Discovery, Inc. I have several collaborations that are well outside my CDD role and one of these may be of broader interest to CDD users. A recent PLOS ONE article “Dispensing Processes Impact Apparent Biological Activity as Determined by [...]
Trending Now – Collaborative Technology!April 26, 2013-The New Trend in Science – Collaborative Technology! Collaborative technology has been in place for a decade, yet the trend towards collaboration is only now becoming a hot topic. David Raths article in KM World “Knowledge-sharing platforms emerge from life science research collaboration” provides a plethora of examples for this. Established companies likeCollaborative Drug Discovery have [...]
CDD to Present at World Malaria Day EventApril 23, 2013-
CDD will be presenting a talk and two posters at a Zagaya World Malaria Day Event this Thursday (April 25) in Emeryville. Although the case studies and examples are for Malaria, it is worth noting that the CDD Vault technology is "therapeutic area agnostic" and thus equally applicable to commercial applications. Here is the full program...
CDD Vault Update: Write APIApril 19, 2013-This release rounds out CDD’s Application Programming Interface (API). With fine-grained write access to molecule and batch objects, the API now provides bi-directional communication between the CDD Vault and your other tools. Link your ELN directly to the CDD Vault, combining the flexibility of ELN reaction capture with the SAR tables and search capability of [...]
Elsevier Acquisition of Mendeley by Mendelspod Plugs CDDApril 17, 2013-Theral Timpson had a humorous blog about open science in light of the Elsevier acquisition of Mendeley.
The funniest quote from one commenter compared it to "Haliburton buying Green Peace."
In his article, there was a concise description of how CDD spans the commercial private and external domains required for drug discovery IP...
Kinome SAR for Collaborative Drug DiscoverersApril 4, 2013-
Among the many valuable resources available at ChEMBL is the Kinase SARfari subset. To make this data available in the CDD interface, we took the core table of Kinase SARfari and merged it with another key table from the ChEMBL database, providing a field describing the assay utilized in each record in much greater detail than is available in native SARfari. We have now made this merged dataset available via the CDD interface. In this new dataset, we have created 400 protocols, where each protocol represents one of the 400 kinases in the SARfari database. This organization allows users to search by molecule, substructure, kinase target, or assay result. This allows one to...
CDD Vault Update: Prêt à importerApril 3, 2013-Prêt à importer Have you ever tried to start an import, only to find the vault locked by another user’s import? Well, no more! Now your vault is always ready to import! Map And Queue Imports At Any Time You can now map and queue imports at any time, regardless of other imports in progress. [...]
Happy Birthday CDD!April 1, 2013-“Happy Birthday to you, happy birthday to you, happy birthday dear C-D-D… happy birthday to you.” CDD was founded in April 2004, spun out of Lilly – a little bundle in the cradle then, and…. oh boy….did that kid grow up fast! It was a bit a disruptive, revolutionary child….how so? Let’s look back for [...]
BIO5 Partners with Collaborative Drug Discovery to Manage Burgeoning Internal Compound CollectionMarch 28, 2013-BIO5 Partners with Collaborative Drug Discovery to Manage Burgeoning Internal Compound Collection TUCSON, Ariz., March 28, 2013 — The University of Arizona’s BIO5 Institute Oro Valley (BIO5-OV) has partnered with Collaborative Drug Discovery (CDD), Inc. to use the CDD Vault, a state-of-the-art cloud technology, to capture and securely share BIO5’s drug discovery research data. [...]
World TB Day 2013March 24, 2013-From the desk of Sean Ekins (VP Science) It’s World TB day 2013 and each year we try to put a few words together to raise awareness and highlight recent development. In recent months we have seen a new therapy for TB-MDR approved in bedaquiline. And yet still we need faster cures to battle this [...]
Top 10 ways CDD has democratized informatics technologies for drug discovery researchersMarch 12, 2013-CDD has effectively lowered the “activation barrier” for data archival of low, medium, and even high throughput experiments. Before you can perform analyses or look for trends, data must be imported into your analysis tool of choice. Here are the top 10 reasons CDD makes it easy to get data in, raising adoption rates amongst [...]
Trypanosomal Inhibitors via Target Class Repurposing ProfiledMarch 8, 2013- The most recent data set profiled on CDD Public, called “PARASITES: Inhibitors via Target Class Repurposing”, comes from Mike Pollastri's laboratory at NEU. In this guest-blog post, Mike talks about his publications and data. Our laboratory at Northeastern University collaborates with several parasitology groups around the world, performing neglected disease drug discovery. This shared data set contains the biochemical and cellular screening data for our published work applying the target class repurposing approach. Currently, the published data sets include trypanosomal phosphpodiesterase (TbrPDEB1 and B2) inhibitor...
CDD Vault Update: Readouts-Only Data Import and an API UpdateFebruary 28, 2013-This release introduces a “readouts-only” import option which allows more actions to be performed concurrently in your Vault. The new API gains numerous features in this release with v1.1, and we introduce API extensions for Excel, Pipeline Pilot, and KNIME. Readouts-Only Import If you are only adding readouts (biology data), choosing this option on Step [...]
CDD at New Orleans National ACS MeetingFebruary 27, 2013-CDD will be at Booth 205 (in the back by concessions) and VP of Science Dr. Sean Ekins will be giving 8 (eight) presentations at the New Orleans National ACS meeting from April 7 - 11th...
CDD will be presenting at the NIH (NCATS) on March 20thFebruary 26, 2013-CDD will be giving a Presentation titled " The Collaborative Drug Discovery Paradigm: Nimble Solutions for Fast Moving Science" on Wednesday, March 20th from 2:00 - 3:00PM at the NIH (NCATS) - detailed in person and webex options for participation are available...
Informatics Considerations at the Dawn of the Antibody Drug Conjugate EraFebruary 25, 2013-Congratulations to Genentech/Roche-ImmunoGen on the FDA Approval of Kadcyla (Ado-Trastuzumab Emtansine), an Antibody-Drug Conjugate for Her2-Positive Metastatic Breast Cancer Antibody-Drug Conjugates (ADCs) combine the best of Nature’s capacity to rapidly evolve specificity with Science’s capacity to deliver specifically designed functionality. There are fascinating, unique ADC SAR (Structure Activity Relationship) informatics representation and optimization challenges when [...]
From CDD Vault to the TB Mobile app: helping Tuberculosis researchersFebruary 19, 2013-Guest blog by Dr. Alex M. Clark, Molecular Materials Informatics, Inc. What do you get when you combine a company with an online collaborative chemistry sharing platform, a startup dedicated to producing cutting edge apps for chemistry, a consultant with deep domain knowledge and lots of ideas, a researcher with access to valuable data, and [...]
Be Our Valentine at the TriConference Feb 14th in San FranciscoFebruary 1, 2013-“If you’re going to San Francisco, be sure to wear some flowers in your hair” Feb 13-14th, CDD will be in force at the Moscone Center in San Francisco for the MMM Triconference at Booth #506 (to your right after entering the Exhibit Hall by the food and beverages, you can register for the Exhibit [...]
CDD Vault Update: Batch Fields, aka Configurable Registration RulesFebruary 1, 2013-CDD’s BFs are here. Despite the pop-culture “best friends” acronym, BF stands for Batch Fields, but we feel that they will become your best friends soon enough! Batch fields allow for customization of molecule registration rules to suit each vault’s needs. They apply to vaults with and without formal chemical registration, and are fully integrated [...]
Four new public data collections to support drug discovery for Chagas diseaseJanuary 17, 2013-Chagas disease is a silent and slow killer. Children in poor, rural areas of Latin America are commonly bit by “kissing bugs” and infected with a parasite called Trypanosoma cruzi. During the initial infection, most children have only mild symptoms and recover without treatment. Unfortunately, in many cases the parasite is not really gone, it’s [...]
Bedaquiline approved by FDAJanuary 14, 2013-The first Tuberculosis drug in 40 years! The FDA just last week approved the first new treatment for tuberculosis in 40 years, Bedaquiline (also known as Sirturo, TMC207 or R207910). This drug was discovered via the screening of 70,000 compounds for activity against M smegmatis, a more rapidly growing and manageable mycobacterium compared with M. [...]
Bedaquiline backed by FDA panelDecember 2, 2012- (TMC-207) was backed by the FDA panel that has been reviewing it since late June. Hopefully it will be approved by the FDA in due course because then it becomes the first drug approved for tuberculosis in well over 40 years. While this is terrific news for patients, we need additional molecules in the pipeline because elevated liver enzymes and QT prolongation were observed...
Crowdsourced Funding for Scientific ExperimentsNovember 29, 2012-Congratulations to Dr. Ethan Perlstein at Princeton. In addition to doing innovative science, he has been innovating on aspects of science touching the Internet and Funding. His lab raised over $25,000 on the crowdfunding site RocketHub for their basic research project. Ethan and his collaborators at Columbia are studying the subcellular distribution of radioactive amphetamines [...]
Michael Siani-Rose Brings Diverse Talents to CDDNovember 27, 2012-Mr. Michael Siani-Rose brings his successful track record at Affymetrix, Chiron, Kosan, and Gryphon to CDD. Michael Siani-Rose (CDD Informatics) was most recently President of Cell Therapy Company Theregen. Of particular relevance for CDD, with the emergence of Antibody Drug Conjugates and informatics standards such as HELM from big pharmas, Michael Siani-Rose co-published with SMILES [...]
CDD’s software architecture advantage, part IIINovember 27, 2012- Other lessons we learned at CDD from running our multitenant system since 2004:
The CDD Vault as a multitenant architecture evolved based on the user community’s feedback and real needs.
CDD Vault Update: Say Hello to the New APINovember 20, 2012-For those of you that have been eagerly awaiting a way to connect your CDD data repository to other applications— the beta version of the API is here for your testing and coding pleasure! In addition to the Application Programming Interface, we’ve also updated the search results display and the handling of units of measurement. [...]
2012 Drug Repositioning Conference HighlightsNovember 8, 2012-
The second annual Drug Repositioning and Indications Discovery Conference was held again in the San Francisco Bay Area on Oct 23-24, and similar to last year, Dr. Barry Bunin chaired an exciting panel discussion. Perhaps co-hosting this Drug Repositioning Summit will become an annual tradition for CDD!
This year's distinguished panelists included Dr. Christine Colvis, Dr. Christopher Lipinski, and Dr. David Cavalla.
Drug Discovery Informatics Veteran Joins CDDNovember 5, 2012-Dr. Michael Travers brings a reproducible track record of commercially successful, informatics innovation to CDD’s strong technical team. Dr. Travers’ broad bioinformatics and chemoinformatics experience adds an eclectic wind to CDD’s sail. Dr. Michael Travers (CDD Software Design) hails from SRI International’s Bioinformatics Research Group, where he worked on developing software tools to support [...]
Using the CDD Vault as collaborative lab inventory system – an exampleOctober 26, 2012-
Three years ago the Martin research group at the University of Texas, Austin worked with Collaborative Drug Discovery to establish and maintain a chemical inventory for over 3,000 compounds. This online inventory application is easy to set up, maintain, and use.
CDD’s software architecture advantage, part IIOctober 24, 2012- Software evolves rapidly. We all get updates and upgrades of operating systems, bug fixes, security patches, new security software, new features at an ever faster pace. This is a big plus for customers of a multitenant application because all of the updates, latest security features, and new functionalities can be implemented quickly without interfering with each client’s implementation.
Rare Disease Challenge – Be HEARDOctober 19, 2012- Assay Depot and Rare Genomics Institute Unite 19 Life Science Companies to Launch a Rare Disease Research Competition. We at CDD are proud to be part of the Open Science Challenge with Assay Depot.
Introducing TB MobileOctober 16, 2012-At CDD, we are focused on novel strategies for developing inhibitors of Mycobacterium tuberculosis (Mtb) as tuberculosis (TB) drugs. Tuberculosis kills 1.8 million people every year (~1 every 8 seconds). We are introducing TB Mobile that displays molecule structure and links to the bioinformatics data on >700 molecules screened versus Mtb and their targets.
CDD releases the first free mobile app for tuberculosis researchers: TB MobileOctober 16, 2012-Burlingame, Calif.—Oct 16, 2012—Collaborative Drug Discovery (CDD), a provider of a web-based collaborative drug discovery software platform, announced they have launched a mobile app for iOS that can assist tuberculosis drug discovery researchers...
CDD Vault Update: Smörgåsbord!October 12, 2012-This release has something for everyone, from project managers to vault admins, and from informaticians to lab techs. Dashboard Reports As a project manager or a lab’s PI, you want a quick summary of your group’s progress. One click away from the Dashboard is the new Reports tab, which shows your team’s productivity over the [...]
Dr. David Matthews, Pathway Therapeutics, Vice President, Drug Discovery and Exploratory DevelopmentOctober 10, 2012-"So I actually started out life as a physicist. My undergraduate degree was physics and during that time my undergraduate tutor was Professor David Blow, who was at Imperial College where I did my degree. He was one of the pioneers of x-ray crystallography, sadly passed away a few years ago, but I would say that David was certainly instrumental in fostering my interest in biology and as I went through my undergraduate degree, I realized that this was a field that was fascinating to me, that I really wanted to get into. So I guess that would be the first turning point was in making the decision to mutate from a physicist into a biologist."
Collaboration, GrantStorming, and You – Oh My!October 7, 2012-
I recently had the pleasure of discussing the parallels between art and science with Theral Timpson at Mendelspod.
Around eight minutes into the interview, I described how web-based software is art. And taken as a whole, the Internet is arguably humanity's greatest collaborative work of art.
What's the pragmatic relevance for busy drug discovery scientists and business people...
CDD Welcomes Charlie Weatherall to Scale Accounts ManagementSeptember 28, 2012-Press release BURLINGAME, Calif., 27 Sept 2012 — Collaborative Drug Discovery (CDD) announces the addition of Charlie Weatherall to magnify CDD’s focus on its Community, further promoting the widespread acceptance of CDD’s platform among academic, government, biotech and pharma researchers. Prior to joining CDD, Charlie Weatherall worked with industry-leading scientific software companies such as MDL (dating [...]
CDD’s software architecture advantage, part I of IIISeptember 20, 2012-
There is a heated debate in information technology regarding whether single tenant or multitenant applications are the way to go. What is the “real cloud” vs. “private cloud” (or “fake cloud” as Marc Benioff, CEO and founder of Salesforce.com, calls it)? This debate has spilled over into drug discovery informatics. Let’s explore the differences and then discuss the pros and cons for both options.
Molecular Medicine Triconference 2013 in San FranciscoSeptember 11, 2012-Dr. Barry Bunin will Present and Chair the "Collaboration and Externalization" at the 5th Annual Integrated R&D Informatics & Knowledge Management Channel.
P.S. By popular demand, CDD will be doing our one cool SmartBoard to CDD Larger than Life at the exhibit (Booth #506) right by the ice cream...and we'll be handing out the equally popular Baby CDD Onesies (for if you or anyone you know was ever a baby:).
“The Collaborative Drug Discovery Paradigm” at SLAS2013September 10, 2012-Dr. Barry Bunin, CEO of Collaborative Drug Discovery at SLAS2013 Dr. Bunin will be presenting at The Society for Laboratory Automation and Screening (SLAS) Second Annual Conference and Exhibition in Orlando, FL, January 12-16, 2013. During the session on “High Performance Computing for Laboratory Data Analysis” Dr. Bunin will be presenting his abstract titled “The Collaborative [...]
The 2nd Annual Drug Repositioning & Indications Discovery ConferenceSeptember 10, 2012-Dr. Barry Bunin will chair a panel & present at The 2nd Annual Drug Repositioning & Indications Discovery Conference in San Francisco Oct 23rd - 24th. The Panel is titled "A New Era for Drug Repositioning: How Successes and Partnerships are Changing the Drug Development Process"
Panelists include:
Christine M Colvis, Ph.D., Program Officer, National Institutes of Health, National Center for Advancing Translational Sciences (NCATS)
Christopher Lipinski, Ph.D. (virtual presenter), Scientific Advisor, Melior Discovery
David Cavalla, Ph.D. (virtual presenter), Founder, Numedicus Ltd., Principal, ATPBio
In addition to Chairperson: Barry Bunin, Ph.D., CEO & President, Collaborative Drug Discovery, Inc.
CDD Vault Update: Escape from the Dose-Response ThicketSeptember 6, 2012-Before we introduce our next major feature release, here is a collection of small but helpful changes to CDD. Escape from the Dose-Response Thicket When a compound has been assayed many times, its dose-response plot can become an impenetrable thicket of curves. As of this release we only show the curves that match your search [...]
Eric Springman, Ph.D., Celtaxsys CSOAugust 30, 2012-"It’s just amazing how science comes and goes in waves. Some of that is related to the tools that you have at your disposal, but when I started out in discovery science and my graduate work and post-doc, particularly the innate immune system, but neutrophils, and this is where I dwell right now, so it’s pretty fascinating to me how it’s coming around. Neutrophils were just viewed as pretty unsophisticated dumb cells in that they were, as we called them, terminally differentiated, which had a lot of implications to it, that they just basically couldn’t think anymore as cells think, they were just preprogrammed to do something and then die. And that really has turned around on its head to where even the cells that we have thought of for a long time now, for the last 20 years as primitive, are actually not at all, they’re very sophisticated cells."
Mendeley-CDD Barry Bunin InterviewAugust 20, 2012-
There is a growing ecosystem of collaborative tools for doing science, CDD's Barry Bunin spoke with our colleagues at Mendeley about CDD's role in the ecosystem, his vision for the brighter future and everything in between. Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research.
CDD Vault Update: Collections PolishAugust 17, 2012-With this release, we are polishing up molecule collections by adding two nice cherries on the top! Explore Imported Data You can now see all registered molecules and associated protocol data from a single imported file with one click. Once a data import is committed, click on the “Explore imported data” link to see the [...]
CDD Announces $1M Phase 2 STTR Grant with SRI InternationalAugust 16, 2012-
Collaborative Drug Discovery (CDD) is in a unique position for drug discovery grants because of the CDD business model precluding ownership of Drug Discovery IP, as well as the complementary chemoinformatics and collaborative web-software capabilities.
Because of the heterogeneity of biological therapeutic areas, targets, hypotheses, and screens, together with the increasing importance of informatics and collaboration, the door is now open for numerous similar at a meta-level, yet completely different and novel in the specific collaborations. Directly contact CDD CEO Barry Bunin for ideas on projects that could benefit from a collaborative, data driven approach to take “good ideas to great”.
National Institute of Allergy and Infectious Diseases Awards Grant to Continue Development of Computational Tools for Tuberculosis Drug DiscoveryAugust 16, 2012-The National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health, has awarded a second grant to Collaborative Drug Discovery, Inc. and SRI International to continue joint development of an information repository and software to identify novel therapeutics for tuberculosis (TB).
The Phase II Small Business Technology Transfer Research (STTR) grant will support the next two years of research and focus on extending a systems biology-cheminformatics approach to develop molecular mimics and computationally evaluate them for drug efficacy.
CDD Vault Update: 1536 wells of happinessAugust 8, 2012-We interrupt our regularly scheduled releases to announce 1536-well plate support. We just couldn’t wait. Import your plate data and CDD will automatically assign the correct plate size: 96, 384, or 1536-well. The new size is fully supported, including molecule plates maps, control layouts and data normalization, heat-map visualization and plate scatter plots with control [...]
Migrating legacy biological and chemical data into the CDD VaultAugust 7, 2012-
If you have an old drug discovery informatics system and it is full with data – but the system is not well maintained or supported any more or too expensive for your budget, then you have a good reason to get new data management software.
You may however be really concerned about the change because you don’t know what to expect.
CDD Vault Update: Cherry-Pick Your Search ResultsAugust 1, 2012-Have you been looking at your screening results, thinking to yourself “If only I could choose the first, the fifth, and the five hundred and sixty-first molecule from this list to add to my collection”? Well, maybe you haven’t yet, but we think you’ll find yourself wondering how you ever survived without these handy green [...]
Assay Depot Partners with AstraZeneca to Launch Virtual Research LaboratoryAugust 1, 2012-
This press release came in yesterday and we thought that this is so exciting that we wanted to blog about it. Congratulations to both, Assay Depot and to Astra Zeneca!
Why are we at CDD getting so excited about this particular news? Because Virtual Research is the future and some companies are not just talking about it but actually doing something for real commercial projects like this one.
Congratulations to Onyx Pharmaceuticals!July 24, 2012-
Congratulations to Onyx Pharmaceuticals on the accelerated FDA approval of Kyprolis™ (carfilzomib) for Injection, a proteasome inhibitor for the treatment of patients with multiple myeloma.
Read the official press release.
What’s the antidote for big data pains at HTS Core Facilities?July 23, 2012-
Originally a province of the pharmaceutical industry, drug discovery has become firmly entrenched in the academic domain in the recent years too. Operating on a smaller scale than in pharma, academic and non-profit drug discovery has become possible with High Throughput Screening (HTS) Core facilities within the university.
Traditionally, most universities share many types of Cores, such as animal facilities, mass spectrometry, and the like, and now the need for HTS cores has become a priority. The clients of such facilities are typically basic biology and chemistry investigators who have the funding, but lack the necessary technical expertise or instrumentation to fulfill their research needs.
CDD in TB Biomedical Computation ReviewJuly 20, 2012-CDD's TB drug discovery collaborations spearheaded by Dr. Sean Ekins were included in Katharine Miller's Biomedical Computation Review Article titled:
"Where Tuberculosis Meets Computation: 10 Points of Intersection, How computation offers a window into a disease often described as a black box."
CDD to Sponsor SERMACS 2012 Catalyzing Sustainable InnovationJuly 18, 2012-Dr. Sean Ekins will present at and CDD is sponsoring:
SERMACS 2012
Catalyzing Sustainable Innovation
14-17 November 2012
Raleigh Convention Center, Raleigh, North Carolina
Quite a Catch!July 16, 2012-
In June 2012, Phil Crews, Distinguished Professor of Chemistry at the University of California, Santa Cruz, delivered his last official “Introduction to Organic Chemistry” lecture after 42 years of teaching. Literally thousands of students have benefited from his dedication to education! This retirement from academia is only partial as he plans to continue his research in chemistry of marine natural products that began in 1974 after perusing a book entitled Poisonous and Venomous Marine Animals of the World. From this book he learned that extracts from sponges exhibit antibiotic and anti-parasitic properties but their chemistry is largely unknown. His imagination captivated, he decided to embark on the adventurous research path at UCSC that continues to be highly productive nearly forty years later.
Virtual Pharma, Externalization, FIPnet, VIPCO – like gravity, you can fight it but you will lose (Part 4 – Scalability)July 16, 2012-
Support is different with CDD. And it comes down to economics. Traditional database and ELN solutions have required high support costs - often with staff on site and costs as high or higher than the purchased technology.
CDD from day one has supported globally distributed groups via the web and phone. In this regard, a large academic user base is particularly noteworthy. An old joke among Vendors is that academics (due to their highly independent nature and budgets) traditionally require twice the support for half the budget. One needs to be 4x more efficient to really effectively support this marketplace. Yet CDD has thrived with users in the academic community.
CDD Vault Update: Unions, Complements, and Exclusive Disjunctions! Oh My!July 6, 2012-Unions, Complements, and Exclusive Disjunctions! Oh My! In this release we round out collection-based search with “Not In”, “OR” and “XOR” logical operations that may be performed on multiple collections. And if you accidentally added a molecule to a collection, you can now remove it and keep your collection current. Complements Remember how you can [...]
How to do more with less = Science Exchange + existing expert academic capacityJune 30, 2012-
At CDD we keep a close eye on the space where science, technology and collaboration meet. In this context we want to introduce “Science Exchange” to you, our user community. Barry Bunin (our CEO) met Elizabeth Iorns, the CEO and founder of Science Exchange at the Science Startup Conference
.
Virtual Pharma, Externalization, FIPNet, VIPCO – like gravity, you can fight it, but you’ll lose (Part 2 – Simplicity)June 26, 2012-
CDD's byline "Archive, Mine, Collaborate" has "Archive" as the foundation. Through an intuitive graphical user interface (GUI), configurable data space, intelligent mapping algorithms, and saved templates, CDD significantly lowers the activation energy for data archival, and therefore compliance on the part of the end-users. How many people have you met that get excited by data entry?!
Virtual Pharma, Externalization, FIPNet, VIPCO – like gravity, you can fight it, but you’ll lose (Part 1)June 21, 2012-
Yesterday's expensive FIPCO (Fully Integrated Pharmaceutical Company) model has been replaced with today's FIPNet (Fully Integrated Pharmaceutical Network) aka VIPCO (Virtually Integrated Pharmaceutical Company) models. What does this really mean? What are the pitfalls when implemented poorly? What is the potential upside? Which people and technologies will win in this new environment?
CDD Vault Update: More Collections and Detail Pages CleanupJune 20, 2012-This release introduces some additional Collections goodies as well as few usability enhancements for the the molecule, protocol, run, and plate details pages. Collections Intersection You can now search for all molecules that are in two or more collections (AND). New Collections Tab on Molecule Page Here you can see the collections that include this [...]
Collaboration as the key to turning around the drug discovery business (Part 12)June 18, 2012-
Ubuntu is defined by Wikipedia as "an African ethic or humanist philosophy focusing on people's allegiances and relations with each other." The idea is that we become richer and derive meaning specifically (even primarily) via our interactions with others. Richer personally. What does Ubuntu have to do with modern technology, business, economics, and drug discovery?
CDD Presentation at StartUp ScienceJune 12, 2012-StartUp Science is dedicated to strategic platforms and applications dealing with what could be best thought of as “Meta-Science Tools,” disruptive technologies and approaches which will make the entire innovation system function more effectively for all stakeholders.
Dr. Joel Freundlich, UMDNJJune 12, 2012-"When you see that activity in a mouse model with the compound that you designed and made and ushered through those early stages, that's really, really exciting... We use CDD Vault all the time for programs where we are evolving structure activity relationships, understanding how a small molecule modulates the target. We are able to track those changes in both graphical and numerical ways seeing how structure influences inhibition of a target. That is just incredibly valuable to us, together with the ability to share the information amongst many different collaborators whom I'm really privileged to have. It is extremely important to exchange data in a seamless fashion. And there is the immense amount of public data that's been archived on CDD Vault."
CDD Vault Update: Molecule CollectionsMay 21, 2012-Have you ever wished CDD tracked your lead molecules or allowed you to restrict searches using a list of molecules or even combinations of lists? Wish no more: we are introducing molecule collections. With this first release, you can create collections and search using one collection at a time. Even better, the next 3 releases [...]
Collaboration as the key to turning around the drug discovery business (Part 11) – The futureMay 11, 2012- The prerequisite to enable the efficiencies of integrated specialization, are secure, trusted collaborative platforms. Mechanisms are required that balance allowing maximum collective contributions, with maximum control of intellectual property ownership. Fortunately, technologies are emerging in this area to allow what was previously impossible, to become routine. Platforms like LinkedIn and Facebook, with rich, flexible [...]
The Collaborative Discovery of a new subatomic particleApril 28, 2012-
The CMS collaboration described the first observation of an excited, neutral Xi_b baryon, a particle made up of three quarks, including one beauty quark.
Although the key experiments took place at the CERN Large Hadron Collider, researchers from all over the world participated intellectually. The drug discovery community is poised to reap the same benefits by watching how the forward-leaning physics community embraces the growing importance of internet accelerated scientific collaboration.
CDD CEO Dr. Barry Bunin Discusses Collaborative R&D with Hassan Masum at the Results for Development InstituteApril 26, 2012-Hassan Masum’s interview with CDD CEO Barry Bunin was posted on the Results for Development Institute blog as part of the “Global Health R&D Policy Assessment Center Project” funded by Bill & Melinda Gates Foundation Transcription of beginning of the interview Hassan Masum Barry, thanks so much for speaking with us today. What is the [...]
Collaboration as the key to turning around the drug discovery business (Part 10) – Learning from eBay, NASDAQ, Airlines, & HollywoodApril 25, 2012- Airline businesses provide an economic multiplier effect for all users that greatly exceeds the margins of the airlines. Many airlines have little to no margins, but it is hard to imagine a modern society without convenient air travel today.
In Hollywood, typically 3 or more partners work together to bring a visionary blockbuster to market, in contrast to the historical approach for blockbuster drugs.
For our industry, the key emerging question is how can consortia of industry, academia, foundation, and government intellectual property guardians evolve a mechanism that allows similar efficiencies in drug discovery?
CDD Vault Update: Spring Cleaning Release #3April 23, 2012-For this third installment, we introduce the highly coveted ability to edit salt data for batches, and a simplified workflow for registering new batches in registration vaults. Other enhancements include a standard deviation calculation for averaged data, as well as a black and white printing option for structure images. Simplified Batch Registration (For vaults that [...]
Stephen Bergmeier: From Shoebox to the Cloud, Collaboration Then and NowApril 19, 2012-"…I have sitting on my desk a shoe box kind of box and it’s got little four by six file cards and on each one of these four by six file cards I have a structure drawn and it’s got a compound identifier and we have someone’s name on there as the person who made the compound and on the various cards there are sort of little pencil marks indicating that we sent so much of it to somebody or we looked at it in a particular assay. And so, you know, actually this is another one of the reasons I really like CDD Vault, is I’m getting rid of my shoeboxes of file cards."
SFSU Center for Computing for Life Sciences “Data for Decision Making” PanelApril 16, 2012-This seminar, in the format of a panel discussion, will provide insights and explore issues regarding management of one’s data, sharing data with teams and enterprise-wide knowledge bases, and using data from the web.
Panelists
Barry Bunin - President & CEO, Collaborative Drug Discovery
Erich Gombocz – VP & Chief Scientific Officer, IO Informatics
Dominic John – Product Marketing Director, Accelrys
Joseph Mulvaney – Informatics Specialist, Small Molecule Discovery Center, UCSF
Moderator: Bob Dunkle – A.B.E.S Partners
Open, Collaborative, & Private FundingApril 10, 2012-Following up on our Open, Collaborative, & Private Data and Model posts… Best of all, the BMGF included a collaborative approach leveraging open data (available from MMV and CDD) in their recent grand challenges which means the community will be able to see for the first time what happens with real dollars behind these [...]
CDD Vault Update: Spring Cleaning Release #2April 6, 2012-This second installment of our Spring Cleaning series brings you two highly requested enhancements. Read on! Exact Keyword Search By default, molecule keyword searches now return results that match your terms exactly. This allows you to find a precise list of molecules using molecule names, user-defined fields, or any other combination of keywords. Of course, [...]
Open, Collaborative, & Private ModelsApril 5, 2012-SAR, QSAR, and Collaborations CDD welcomes the modeling community to the party! After pioneering the open Models meme in 2010 by demonstrating the statistical equivalence of ubiquitous open source descriptors and models available for free to expensive commercials QSAR model tools that often cost millions of dollar…it is interesting to see that other groups [...]
Open, Collaborative, & Private DataApril 3, 2012-Welcome to the Party! CDD has supported the complementary virtues of public with private sensitive drug discovery data since the Oct 26th, 2007 publication of “1721 FDA approved drugs with designated indications, sponsor name, and chemical structures” with Dr. Christopher Lipinski. To emphasize the security and privacy, even on a subconscious level, the platform [...]
CDD – 8 years in the cloud. Really.April 1, 2012-Our cloud based drug discovery software celebrates its 8th birthday From the desk of Sylvia Ernst – CDD Sr. Director Community Growth Yes – it is April 1st – and yes – it is true. CDD was founded on April 1st 2004 and started running a web-based database to join molecules with their many bioassay data. [...]
CDD Vault Update: Spring Cleaning Release #1March 30, 2012-Instead of adding the next major feature, we’re pausing for a moment to polish the existing application and implement your most commonly requested small changes. This is the first in a series of releases intended to make your day-to-day experience with CDD more enjoyable. Dose-Response: Better axes and labels X-axis labels now show concentration [...]
World TB Day 2012March 24, 2012-From the desk of Dr. Barry A. Bunin – CEO, Collaborative Drug Discovery (CDD): Raise awareness, overcome resistance, shorten treatment, optimize drugs to minimize the future human toll from Tuberculosis this World TB Day 2012. I wish it were not true, but unfortunately, last year’s blog on World TB Day 2011 by Dr. Sean [...]
Why you need to stop meeting in-person now for doing business!March 22, 2012-Work 3.0 is here and competing with you! From the desk of Sylvia Ernst, Ph.D – Sr. Director Community Growth at CDD Just recently LinkedIn featured this article: http://www.inc.com/rene-siegel/five-reasons-you-need-to-meet-in-person.html and it got raving comments. But let’s think this through for a moment. I would counter that in person meetings – and a corporate culture [...]
CDD Vault Update: Normalize Dose-Response Data? Yes We Can!March 16, 2012-With this highly anticipated release, you can start importing raw data for your dose-response experiments, and let CDD calculate % activity based on controls. This is building on existing functionality of calculating EC50 based on % activity. We hope you will be able to import dose-response data into CDD as they are generated, eliminating the [...]
Why you can’t avoid the “web” any longer for your Drug Discovery dataMarch 8, 2012-Surfing two disruptive waves: “The Cloud” and “Collaboration” From the desk of Sylvia Ernst – CDD Sr. Director Community Growth Remember those days? A while ago the computing world changed from Terminal/Host systems to Client-Server technology; that was in the early nineties. Terminal/Host required an expert for data input into a terminal and the data were processed [...]
Collaborative (Rare Disease) Drug Discovery DayMarch 1, 2012-Today is Rare Disease Day. In a way, every day for CDD and the CDD community is Rare Disease Day. Why? Effective collaborations are the key to efficient drug discovery on a tight budget. And by definition, all rare disease drug discovery must be done on a tight budget leveraging a small number of [...]
CDD Vault Update: À la Carte Commit for Data ImportFebruary 29, 2012-This release introduces the ability to selectively reject/accept all events of a specific type. Sometimes, a data import can have some unexpected (and undesired) consequences. Before today, if you wanted to prevent those consequences, your only choice was to cancel the import, correct the file and re-upload. This was fine if you were only dealing [...]
CDD’s Leadership Illuminated in Recent Nature & Chemistry Biology PerspectivesFebruary 20, 2012-CDD’s leadership driving drug discovery in the cloud was illuminated in recent Nature and Chemistry Biology perspectives. The Nature article highlighted the historic first time big pharma shared sensitive full drug discovery screening data on ChEMBL, Pubchem, and CDD. “Two years ago, GlaxoSmithKline (GSK) announced that it would release details of about 13,500 molecules that [...]
Dr. Michael Pollastri, Northeastern UniversityFebruary 15, 2012-"…being able to basically have a one-stop shop for people in my group to go and actually look for their data across multiple projects and also to have my collaborators to be able to just sort of access in an easy way the data that’s relevant to their projects without making it a really sort of arduous search to do. I mean basically it’s almost like the Project’s concept was designed for projects – for labs like mine."
Collaboration as the key to turning around the drug discovery business (Part 8) – StandardsFebruary 14, 2012-Collaborative drug discovery platforms are broadly applicable across therapeutic areas, targets, and teams. All drug discovery projects have numerous conserved technical and commercialization hurdles. The regulatory, scientific, and economic foundations of drug development are conserved. Apart from the fascinating, idiosyncratic manifestations arising from different molecules, targets, assays, and teams…there are common, systematic technical challenges [...]
A More Enlightened Approach to ADME?January 27, 2012-Animals as surrogate test subjects for humans are becoming less desirable as the effects of cost, negative social pressure, and the reality that animals are not always accurate predictors of human outcome move research to consider alternatives.
CDD Vault Update: Small Changes to Start the New YearJanuary 20, 2012-Small Changes to Start the New Year CDD has been focused on a number of long-term projects over the last few months, but we’ve managed to find some extra time to provide the following updates: Customers with unparseable data files can now use the CDD Message board to exchange these files with CDD staff. When [...]
Collaboration as the key to turning around the drug discovery business (Part 7): Collaboration = LeverageJanuary 20, 2012-Linking scientific teams and their projects sounds like an obvious, excellent idea. Mutually beneficial exchange of information offers a means of accelerating the efficiency of drug discovery. At CDD over the last 8 years we’ve been obsessed with engineering a collaborative, web-based platform that allows anyone to leverage other scientists’ drug discovery results while maintaining [...]
Finding a cure for TB: The world is a virtual lab and the cloud is the limit!January 14, 2012-From the desk of Sylvia Ernst, Ph.D – Sr. Director Community Growth at CDD Neglected disease research is one of our passions here at CDD – Malaria and TB in particular. Yesterday, I (Sylvia Ernst) came across this well written Wired Magazine Article that references back to a related recent Times of India Article on TDR (Totally [...]
CDD welcomes the healthcare industry to San FranciscoJanuary 10, 2012-JP Morgan Global Healthcare conference is in town. Investors and entrepreneurs converge on the San Francisco Westin St. Francis during this second week of January in what has become an annual rite of passage for the biotech industry. The suits and smartphones mix science and business at the JP Morgan Global Healthcare Conference. First impressions, [...]
Collaboration as the key to turning around the drug discovery business (Part 6) – Technology can make things easierJanuary 4, 2012- Science is hard. Drug Discovery is hard. Chemistry is hard. Biology is hard. Business is hard. Innovation is hard. Management is hard. Technology can make things easier. Some technologies make a little impact. Other technologies, such as the printing press in years past and the linking of computers via the Internet more recently, have [...]
CDD Vault Update: Enhanced StereochemistryDecember 22, 2011-Key points Relative stereochemistry is a thorny area of cheminformatics. Here are the key points for CDD users: CDD sets the chiral flag to ‘absolute’ whenever you import from SD files or Molfiles. We do this to avoid unintentional duplicate structures and to ensure that structure search is consistent. If you need to record the [...]
Happy Holidays and a Toast to Our Collaborators!December 19, 2011-Happy Holidays from our Community Growth Department here at CDD to you. We love collaborating with you as we travel this new and exciting path together. The path of Collaboration at all levels is an interdependent one. Collaborating outside your four walls to discover new drugs, fast and cost efficient – this was thought to [...]
CDD Vault Update: Enhanced Security OptionsDecember 18, 2011-Two-Factor Authentication In this release CDD introduces an optional second layer of user authentication for groups that prefer added security. While a strong password is sufficient for most groups, a Vault can now require a second authentication step via mobile device or telephone. CDD has partnered with Duo Security (www.duosecurity.com) to deliver this free option, [...]
The beginning of the end of AIDSDecember 15, 2011-The CDD community works on web-catalyzed scientific breakthroughs to accelerate drug discovery for global human health. For AIDS eradication the challenge is social as much as scientific. Antiviral treatments are available and recently studies suggest they are even preventative. A small one-time investment will save lives and significant money long term. As a race, we [...]
We’re Hiring AgainDecember 13, 2011- CDD is searching for an experienced and remarkable grant writer with a successful track record. Multiple internal and external grant projects are available given the large number of CDD collaborations with scientific thought leaders. An ideal candidate would thrive in a unique nurturing ecosystem by refining the best opportunities selected from our growing community [...]
Malcolm Kendall (President & CEO), Indel Therapeutics, Inc.December 9, 2011-"CDD Vault is a G=d-send. We are a virtual company. I’ve got people spread from Montreal to Vancouver to L.A. and we really needed some way to kind of bring it all together and capture the data that we were creating and be able to share and analyze it. So it’s become sort of a critical part of our existence, in a sense. Before we were capturing data on spreadsheets so having a web-served application like CDD Vault, allows you to collaborate real-time with your people, spread across two countries and several time zones. It is easy to use, has lots of features and because of it we can now better use and share the data we are creating."
A CDD Poem – Spreading Some Holiday CheerDecember 5, 2011-I want to discover a drug
With collaborators so trusted I hug
A once in a lifetime “Ah-ha”
Thousands of data points insightfully clawed...
ACS Spring 2012 National Meeting in San Diego March 25 – March 29December 2, 2011-Drs. Barry Bunin and Sean Ekins will present at the ACS Spring 2012 National Meeting & Exposition. Dr. Bunin's talk is on Sunday (Mar 25th) from 2:50 pm to 3:30 pm in Room 26A, Dr. Ekins has 5 presentations.
Molecular Medicine Tri-Conference, San Francisco, February 21-23, 2012November 30, 2011-CDD's Scientific Collaborations Director Dr. Sean Ekins (Mon Feb 20th at 2:30PM) will present a talk titled "Collaborative Drug Discovery TB database (2011 Editors’ Choice Award Winner)".
CDD CEO Dr. Barry Bunin will moderate a panel (Thurs Feb 23rd at 8:30AM) and exhibit at booth #316 at the Cambridge Healthtech Institute's Molecular Medicine Tri-Conference in San Francisco, CA on Feb 21-23.
CDD Director of Operations Kellan Gregory will showcase the CDD Vault for budget sensitive laboratories and large global collaboration at the New Product Showcase.
Virtual platforms & Pre-competitive Collaborations @ the World Pharma Innovation Congress Jan 31 – Feb 2 in SF, CANovember 30, 2011-Drs. Alpheus Bingham (CDD BOD member) and Barry Bunin (CDD CEO & BOD member) will present back-to-back at the World Pharma Innovation Congress and present on a panel to discuss the emerging interdependency between competitive and pre-competitive knowledge in drug discovery together with Dr. Tim Willson, Director of Chemical Biology, GlaxoSmithKline and Dr. Tariq Ghayur, Senior Principal Scientist, Abbott Laboratories.
New data released: Trypanosomal phosphodiesterase inhibitors.November 10, 2011-A new public data set has been released from the neglected disease drug discovery team at Northeastern University (Boston, MA) and the Marine Biological Laboratory at Woods Hole, as reported in the Journal of Medicinal Chemistry this week (DOI: 10.1021/jm201148s). This data set consists of a range of established human phosphodiesterase inhibitors, tested for inhibition [...]
We’re HiringNovember 4, 2011-Here is some refreshing, positive economic news for a change. We’re hiring. We rarely and selectively hire, but if you know someone who is exceptionally qualified please let us know. Here are the current CDD opportunities that oscillate between being actively or passively open for consideration over time: https://www.collaborativedrug.com/pages/employment
CDD Vault Update: Collaboration Privacy: Vault Member NamesOctober 21, 2011-Collaboration Privacy: Vault Member Names While project data has and always will be secure, we are increasing privacy for Vaults that hinge on keeping their collaborator’s names hidden. The enhanced privacy should allow each Vault to invite every single collaborator working on a particular project to CDD. This way, everyone can take advantage of the [...]
CDD hosts data from whole-organism screens for schistosomiasis at the UCSF Sandler Center for Drug DiscoveryOctober 18, 2011-CDD is pleased to host data from phenotypic (whole-organism) screens on the Schistosoma mansoni parasite run at the UCSF Sandler Center for Drug Discovery. CDD now hosts both published [Abdulla et al., 2009] and unpublished screen data on a wide variety of screen collections including those containing compounds already approved for use in humans.
In this guest blog Dr. Conor Caffrey describes his work on the Schistosoma mansoni parasite and invites partners to collaborate in this challenging project.
5 Reasons Why Collaborative Scientists Use CDDOctober 17, 2011-CDD provides Projects inside secure CDD Vaults™ for temporal, spatial, and data-type partitioning capabilities whether it is for a single shared compound or HTS screening campaign. CDD’s lightweight chemical registration and SAR technology and services are economical for those in budget conscious labs to large pharmaceutical companies. CDD supports collaborations from the single lab to [...]
Accelrys Shines a Spotlight on CDD in BioIT WorldOctober 17, 2011- Per the recent write-up by Kevin Davies in BioIT World, we welcome industry leader Accelrys (with many very different products under their umbrella) to the collaborative SAAS space we’ve been focused on for over 7 years. CDD Projects right in collaborative CDD Vaults let you easily collaborate in your natural workflows – no multiple [...]
aDREAM for the International Chemical Biology SocietyOctober 12, 2011-“You may say I’m a dreamer, but I’m not the only one.” – John Lennon, Imagine Scientists are now starting to collaborate to work together to fight diseases in a field that has traditionally been done in isolation, a tipping point was felt this week in Kansas City. Standards and funded infrastructure for collaborative science [...]
CDD Vault Update: Importing Data: More Noteworthy EventsOctober 11, 2011-Importing Data: More Noteworthy Events We’ve fallen in love with the new data import summary, particularly how it reveals exactly what events will occur. It does such a good job of being clear and revealing that it highlighted some cases where we weren’t reporting noteworthy events. This release addresses that, along with many other small [...]
CDD Implementation at the UCLA – CMCROctober 5, 2011-In this guest blog, Dr. Andrew Norris describes how the UCLA – Center for Medical Countermeasures against Radiation (CMCR) implemented CDD. The chief aim of the UCLA CMCR is the discovery and development of novel small molecule drug leads that serve as radiation mitigators in addition to advancing our understanding of radiation toxicity and lethality [...]
Drug Resistance and Emerging Infectious Diseases: Meeting the Challenge- December 12-14, 2011September 28, 2011-Sean Ekins, CDD’s Collaborations Director, will participate in a panel discussion at the Drug Resistance and Emerging Infectious Diseases: Meeting the Challenge conference on December 12-14, 2011 in Baltimore, MD. The panel will take place on Dec 13 at 3:30 – 4:30pm. The panel topic is Business Model Innovation to Support R&D for Effective Antibiotics: Across the pharmaceutical [...]
An alternative business model for drug discovery talk at the Partnering for Cures Conference- Nov 7-8, 2011September 28, 2011-As has become a good tradition, Sean Ekins – CDD’s own Collaborations Director, will present a talk at the Partnering for Cures conference, taking place on November 7-8 at the Grand Hyatt hotel in New York City. The talk is titled “Collaborative Drug Discovery: An alternative business model for drug discovery.” Adopting a standard, collaborative framework would [...]
Open Science Summit Oct 22-23 in Mountain View, CASeptember 27, 2011-Barry Bunin will present at the Open Science Summit on Sunday, Oct 23rd at the: Computer History Museum 1401 N Shoreline Blvd. Mountain View, CA 94043 The full program is here: http://opensciencesummit.com/program/
Life Science Collaboration & Virtualization talk at the PRISME Forum Meeting & Special Interest Group – Oct 17-21, 2011September 27, 2011-Sean Ekins will present a talk at the PRISME Forum Meeting & Special Interest Group, scheduled to take place on Oct 17-Oct 21, 20011 at Biogen Idec, Cambridge, MA. Sean will give a forward looking perspective of the changing landscape of Life Science Collaboration & Virtualization. Biomedical research has become increasingly driven by creating and consuming tremendous volumes of complex [...]
Dr. Thomas J. Magliery, Ohio State UniversitySeptember 27, 2011-Thomas J. Magliery was born in Oak Park, Illinois, in 1974 and grew up outside of Chicago and Indianapolis. He conducted medical genetics research with M. Ed Hodes at the Indiana University Medical Center in Indianapolis, leading to a semifinalist-winning project in the Westinghouse Science Search in 1992. Fast-forward a few years at Berkeley, Scripps and Yale, and Dr. Magliery joins the faculty of the Ohio State University in the fall of 2005 as an Assistant Professor in the Department of Chemistry and the Department of Biochemistry. He is a member of the Ohio State Biochemistry Program, the Biophysics Graduate Program and the Chemistry-Biology Interface Training Program.
CDD Vault Update: A Single-Page QC ReportSeptember 23, 2011-The most critical decision you have to make when importing data in CDD is whether you should commit the data or not. The previous version of the report gave you access to all the information but it did a bad job highlighting the important facts that should drive your decision. The new single-page report groups [...]
CDD NIH Project “Biocomputation across distributed private datasets to enhance drug discovery” Profiled on GenomeWebSeptember 21, 2011-Uduak Grace Thomas, the BioInform editor, published an article today titled:”Collaborative Drug Discovery Bags Phase I SBIR to Build Tools for Sharing Models of Drug Molecules”. It begins, Collaborative Drug Discovery recently received a Phase I Small Business Innovation Research grant from the National Library of Medicine that it will use to develop a method [...]
Collaboration as the key to turning around the drug discovery business (Part 5) – a Monte Carlo SimulationSeptember 19, 2011-There is widespread appreciation that the traditional business model for drug discovery and development is under pressure from all sides. The easier health issues have been addressed, the harder ones remain. The challenges are real. An overemphasis on focusing on immediate maximum ROI for minimal investment in each asset has led to a literal drought [...]
CDD’s Sean Ekins Elected to Pistoia Alliance BODSeptember 15, 2011-Following recent blogs and provocative conversations regarding the Pistoia Alliance we are proud to announce that CDD’s very own Collaborations Director, Dr. Sean Ekins, was recently voted onto the BOD for this organization. We look forward to assisting in the future success of Pistoia and promoting some of the initiatives we have described and believe [...]
What’s wrong with the Pistoia Alliance…and why we’re renewing our annual membership! (Part 2)September 6, 2011-We ended Part 1 of this series predicting, “In the near future, effective collaborations will become the default mechanism for being competitive.” With collaborative technologies where researchers can simultaneously evaluate private, collaborative and public data…the distinction between pre-competitive and competitive drug discovery becomes obsolete. By embracing collaborative technologies using standards for chemical data and [...]
What’s wrong with the Pistoia Alliance…and why we’re renewing our annual membership! (Part 1)August 31, 2011-Pistoia folks have the right attitude (precompetitive work to avoid redundancy), use the right tools (Basecamp), but don’t go nearly far enough. Although clothed in novelty and open mindedness, it is essentially the same vendors and embracing the same approaches, with evolutionary, not revolutionary, advances. The Pistoia Alliance correctly points out the problems in their [...]
Collaborative Drug Repositioning Profiled in the Wall Street JournalAugust 25, 2011-In a highly collaborative study, Dr. Atul Butte and collaborators at Stanford, multiple CROs, and Numedii using public databases plus new algorithms have “found that topiramate, a drug used in epilepsy, might work on inflammatory bowel disease, including Crohn’s disease and ulcerative colitis. Another hit suggested that cimetidine, an ulcer drug, might be effective in [...]
CDD Vault Update: Importing Data with a Simpler Mapper (That Does More)August 22, 2011-You can now provide default values when importing data by adding virtual fields to your file. This change allowed us to remove the bulky Default Values section, presenting a cleaner interface to all users while preserving and expanding advanced functionality. Easily Add Missing Fields To add a default value for every record in your file, [...]
Collaboration as the key to turning around the drug discovery business (Part 4) – Collaboration and InnovationAugust 18, 2011-What is the right type of innovation for successful drug discovery today? How do innovation and collaboration contribute to the success of your drug discovery efforts today? The answers depend upon your strengths, weakness, opportunities and threats (SWOT analysis). As much as there is no single formula for all situations, there are more and less [...]
CDD Founder Dr. Barry Bunin on FounderLYAugust 8, 2011-Dr. Barry Bunin, CDD's founder and CEO, recently gave an interview for FounderLY. In this 2-part interview, he shares his background, how CDD came to be and what drives us.
Collaboration as the key to turning around the drug discovery business (Part 3) – A SolutionAugust 7, 2011-A Solution: Adopting a standard, collaborative framework would lead to more cost-effective drug discovery as a natural consequence of the economic efficiencies of integrated specialization. Collaborative technologies provide a secure mechanism to withhold, partition or selectively share refined IP-sensitive proprietary drug discovery data down to an individual experimental result – regardless of whether the information is internal or external in a single cloud-based database.
E.T. phone homeAugust 7, 2011-NASA scientists found both terrestrial and extraterrestrial nucleotides on meteors in the Antarctic and Australia. The experiments were performed with minimal risk of earthly contaminants. Perhaps, per the immortal words of Joni Mitchell, “we are star dust” after all. Maybe biologists and chemists have underestimated the likelihood elsewhere in the universe of the spontaneous [...]
Nice article on CDD in BioIT World by Allison ProffittAugust 2, 2011-The July-August issue of BioIT World has a nice article on CDD’s work supporting research in the cloud. Here is an excerpt: “Collaborative Drug Discovery has developed a molecular library database to serve a network of over 100 tuberculosis researchers in the U.S. and Europe, helping their users mine and collaborate on tuberculosis data. Their [...]
CDD Vault Update: Importing Data: Faster and Easier MappingJuly 29, 2011-Importing Data: Faster and Easier Mapping We’ve further refined the mapper to make it quicker and more intuitive. Here’s the new design: In addition to the design refresh, we have streamlined the data import process to only three steps. There’s now a link to create a mapping template on step two, in addition to the [...]
Collaboration as the key for turning around the drug discovery business (Part 1) – The ProblemJuly 22, 2011-The Problem: Drugs commercialized today are often discovered in one organization and developed in another. It is a natural outcome of an increasingly expensive and specialized drug discovery process. The investment community and industry as a whole have moved their efforts downstream, focusing more resources on later-stage drug development. This trend has created a crying need...
Alternative Business Models for Drug DiscoveryJuly 22, 2011-Our Drug Discovery Today Editorial "Alternative Business Models for Drug Discovery" is now in press via Science Direct and on PubMed. Contact us for a copy of the article...
Christopher Lipinski – Drug Repositioning Panel Talk TranscriptJuly 20, 2011-Christopher Lipinski Okay. Well I’m very glad to be able to participate in this webinar and what I’m going to do is I’m going to talk about sort of science issues in drug repositioning, and I’m going to really put it in the context of the problems that we have nowadays in drug discovery, [...]
David Cavalla – Drug Repositioning Panel Talk TranscriptJuly 20, 2011-David Cavalla So I’ve just got a few slides here, hoping to pick out a couple of points on Drug Repurposing. The title emphasizes two points, obviously looking ahead but also trying to make use of a retrospective view. So what I’m trying to convey in that title is the idea of seeing a little [...]
Noel Southall – Drug Repositioning Panel Discussion TranscriptJuly 20, 2011-Noel Southall So actually in the interest of time, I might actually skip my slide overview and actually turn this more back into a panel discussion just by referencing some of the points from the previous talks. I think Chris really gave an excellent presentation that raised some really interesting points. But first to go [...]
Barry Bunin – Drug Repositioning Panel Talk TranscriptJuly 20, 2011-Barry Bunin Okay, so I’m going to talk about collaborative platform to drive drug repurposing, which is also a platform in general for drug discovery whether repurposing or not, and one example of a collaboration that we’ve been working with the Bill & Melinda Gates Foundation has been supporting tuberculosis research and recently got nominated [...]
Drug Repositioning Conference HighlightsJuly 20, 2011-CDD attended the Drug Repositioning Conference in San Francisco last week. Representatives from big pharma and specialized drug repositioning companies talked about repurposing as the fastest way to an approved drug by capturing IP and showing differentiation. Barry Bunin chaired a webinar panel with Chris Lipinski, David Cavalla and Noel Southall. If you've missed the webinar, download the talks here.
Pioneering use of the cloud for development of Collaborative Drug Discovery (CDD) DatabaseJuly 20, 2011-CDD are pleased to announce the publication of a chapter in a new book called Collaborative Computational Technologies for Biomedical Research, edited by our Collaborations Director Sean Ekins, Maggie A.Z. Hupcey (previously PA Consulting, Now Novartis Vaccines) and Antony J. Williams (Royal Society of Chemistry) and published by Wiley. Sean blogged on how this book [...]
Dr. Ellen Berg, AsterandJuly 19, 2011-"I was always interested in sort of the bench-to-bedside areas; how do we do a better job of finding new drugs that are actually going to work in people safely."
Thalidomide: Poster Child for Drug RepurposingJuly 7, 2011-To whet the appetite for next week’s Drug Repositioning Conference & CDD Chaired panel on broadcast live via GoToWebinar w/ Drs. Christopher Lipinski, David Cavalla, and Noel Southall, we are sharing thoughts on Thalidomide – the “poster child for drug repurposing”. Thalidomide, infamous for producing so called “thalidomide babies” in the 1950’s when used for [...]
CDD Vault Update: Dose-Response Plots Enhancement GaloreJuly 7, 2011-With this last release in our series of dose-response improvements, we are very excited to introduce the following additions to your dose-response toolkit. Dose-Response Plots Enhancement Galore See All Your Plots First, we have enhanced the way we generate dose-response plots so that the application always displays and exports plots even when the associated compound [...]
The Cause of ADHD…or the Key to Accelerating Human Enlightenment?July 6, 2011-Is the variant of the dopamine-processing gene DRD4 the cause of ADHD (Attention Deficit Hyperactivity Disorder), the key to accelerating human enlightenment – or both? At CDD, we are honored to support researchers’ collective quests to discover new drug candidates. In fields as broad as chemistry interacting with biology, better mining and collaborative tools [...]
Supreme Court 5-4 and 6-3 Victories for the Drug Discovery BusinessJune 25, 2011- Two rulings by the Supreme Court earlier this week provide some positive news for the drug discovery business. The first ruling minimizes patient litigation against makers of generic drugs. Generic drug makers use the same warning label as the initial company that discovered the drug. The court basically says it trusts the FDA’s judgement [...]
“If you miss the train I’m on…”June 22, 2011- …why am I channeling train songs by Peter Paul and Mary this morning? Because today is the 3rd excellent TRAIN series I’ve attended as part of a new program by Faster Cures. I think this type of series points to how information will be effectively shared in our industry in the future. Today it [...]
CDD Vault Update: Dose-Response Improvements Part III: Got Controls?June 14, 2011-Control Lines and Standard Curves Do you screen positive and negative controls in your dose-response protocol? What about standard compounds? With this release, sample plots now include control lines and standard curves when displaying data for only one run. When all positive controls share the same concentration, a positive control line is shown in red: [...]
CDD Vault Update: Dose-Response Improvements Part II: IC50s, MICs and More, Oh My!June 3, 2011-Easier Import Dose-response data is now imported in a two-column format (e.g. concentration and activity) which means you no longer have to pre-define your dose series. This allows for variable concentrations across samples and enables you to import data directly from screening plates. We have deleted all mapping templates for dose-response data, because they no [...]
Jim Wikel, Ex-Eli Lilly, Apex TherapeuticsMay 19, 2011-"I came from southern West Virginia, the coal fields of southern West Virginia, and it wasn’t that common for folks to go to college...when I retired, I was head of Computational Chemistry and Structural Biology with Lilly."
CDD Vault Update: Dose-Response Improvements Part I: Consistency!May 12, 2011-The calculation of dose-response data is now consistent throughout CDD. Previously we would calculate one EC50 for each row of data, but on the plot we would aggregate all the data by batch/run and perform a separate calculation. Now, all dose-response calculations are performed using the aggregate data from each batch/run, so the numbers in [...]
New TB Targets and Molecules Data Available for Public Access Use!May 2, 2011-Our collaboration with SRI is yielding some new public data sets that leverage the small molecules and TB data collected in CDD with the expertise in pathways databases.
TB drugs and leads with targets
TB target database for In vivo essential genes
New Data from the FDA Available for Public Access Use!April 30, 2011-CDD has made publicly available the rare disease research database (RDRD), and examples of FDA approved drugs repurposed using HTS. Look for these new data sets under the Public Data heading of the Explore Data section.
FDA Panel Unanimously Approves Two New Hep C drugsApril 30, 2011- Amid all the angst regarding the high costs of drug discovery, it is refreshing to see two new drugs for Hepatitis C approved by FDA advisory panels. In the past two days the Antiviral Drugs Advisory Committee of the U.S. Food and Drug Administration (FDA) unanimously approved Merck’s investigational medicine VICTRELIS™ (boceprevir) and Vertex’s [...]
NCATSApril 28, 2011-It is not every day that the NIH creates a new center, but the proposed National Center for Advancing Translational Sciences (NCATS) is just that. There is an interesting dialog separating the NCATS fiction from fact here.
CDD Resources for World Malaria Day (25 April 2011)April 25, 2011-Today (25 April) is World Malaria Day. In addition to doing our little part hosting Public Malaria Drug Discovery Data (ranging from the discovery of early anti-Malarial compounds during WWII to GSK’s recent release of enzyme and cell screening data) and supporting researchers’ pre-publication data in private CDD Vaults – here are two sites with [...]
CDD Vault Update: Only Display Matching ReadoutsApril 22, 2011-Too many data point in the search table causing you to go cross-eyed? In this release search results are more precise and compact. Only Display Matching Readouts Now we display only the readouts that match your search criteria. For example, you have tested a molecule several times, but the activity was high in only one [...]
15th Annual Green Chemistry & Engineering Conference, Jun 21-23April 15, 2011-Look for Dr. Sean Ekins of CDD at the 15th Annual Green Chemistry & Engineering Conference in Washington DC on June 21-23. He will be participating in a workshop after the conference, and will give a brief talk on the 24th of June.
MM4TB CM2 Meeting, July 1-2April 15, 2011-Dr. Sean Ekins of CDD will be at the MM4TB CM2 Meeting in Green Park Resort, Tirrenia, Tuscany in Italy on July 1-2 2011.
CDD Wins Prestigious BioIT 2011 Best Practices Editors’ Choice AwardApril 14, 2011-We are pleased to announce today that we have just been awarded the BioIT Editors' Choice Best Practice Award for our work supporting tuberculosis researchers at NIAID and the TB Alliance. This award acknowledges two years of software development and support for TB research groups funded by the BMGF, and is a credit to all CDD users and community members who have helped guide our technology over the past seven years in the cloud.
CDD Vault Update: A Smarter MapperMarch 30, 2011-When importing data, why should you have to tell CDD that your column named “SMILES” contains molecule structures? Shouldn’t CDD be able to figure that out? We now automatically select our best guess for how each header should be mapped, so you only need to click “Apply”. You can always override or ignore the best [...]
Dr. James McKerrow, UCSFMarch 29, 2011-As CDD’s first major customer, Dr. McKerrow guided us in our early days and introduced us to the Gates Foundation, making him perfect for our first CDD Spotlight.
World TB Day 2011March 24, 2011-The Financial Times has produced a special FT health supplement called “Combating Tuberculosis”. This highlights everything from needing more money for the clinical trials, the poor distribution of drugs for multidrug resistant TB and also recent discoveries in the biology of TB. An editorial online also suggests “Tackling TB will be expensive. The price of not doing more will be greater.”
BioIT World Conference and Expo, Apr 12-14March 21, 2011-Dr. Sean Ekins of CDD will be giving a talk at the BioIT World Conference and Expo in Boston, MA on April 12-14.
CDD Vault Update: Use Your Own LingoMarch 4, 2011-Would you rather say “assay” than “protocol”? Does “experiment” make more sense to you than “run”? We now allow the administrators of each Vault to choose their own synonyms for the following terms: molecule, batch, protocol, run,readout definition and readout. The place to set these is under the Settings sub-tab in the Manage Vault section. So track down your Vault admin [...]
CDD Provides Technology in Global Consortium to Identify New Tuberculosis DrugsMarch 4, 2011-Burlingame, CA, March 4, 2011 — Collaborative Drug Discovery, Inc. (CDD; https://www.collaborativedrug.com/) has joined the École Polytechnique Fédérale de Lausanne (EPFL), AstraZeneca, Sanofi-Aventis, the Universities of Pavia, Uppsala and Cambridge, and nearly twenty other research groups from 13 different countries, to form the More Medicines for Tuberculosis (MM4TB; http://www.mm4tb.org/) consortium, which aims to develop new [...]
Collaborative Drug Discovery, Inc. & Royal Society of Chemistry’s ChemSpider Announce PartnershipFebruary 25, 2011-BURLINGAME, CA. and Wake Forest, N.C., February 21st, /PRNewswire/ — Collaborative Drug Discovery (CDD), the provider of the most widely used cloud-based drug discovery software platform on the market and Royal Society of Chemistry’s (RSC) ChemSpider, a leading provider of chemical services and data on the internet, have implemented two-way linking of public compounds that [...]
CDD Vault Update: Data Upload ImprovementsFebruary 14, 2011-Importing your data is a critical and often tricky first step when using CDD. This is the first in a series of releases aimed at making data upload faster and easier. Look for the following: Create a run on-the-fly! Yes, you read correctly, you can now create a run on step 2 of the Import [...]
CDD Vault Update: And… the Portal is gone!February 8, 2011-The sidebar now allows you to control exactly which data (public and private) you want to see, all from a single interface: no more tiers, different versions of pages, or disappearing edit links. We’ve moved all searches you saved at the portal level into your Vault to provide a seamless transition. If you’re still using [...]
CDD Vault Update: Portal RemovalFebruary 3, 2011-We are happy to announce that we have started working on removing the portal. With projects, there is no longer a need to keep the portal, and frankly, we feel like the overall CDD experience will be much improved once it’s gone. We encourage anyone with concerns to contact support. In the true spirit of [...]
CDD Vault Update: Performance and Improving Load TimesJanuary 25, 2011-This release focused heavily on performance. We targeted improving load times on the protocols, molecules, and runs pages. A few other improvements include: Tautomer detection is always tricky in registration systems. To help, the application will now warn you when it detects a possible tautomer of an existing molecule in your Vault. The warnings can be [...]
Collaborative Innovation in Biomedicine, Apr 5-6January 21, 2011-Dr. Sean Ekins of CDD will be giving a talk at the Collaborative Innovation in Biomedicine conference in Philadelphia, PA on April 5-6. Stay tuned for more details!
ACS Spring 2011, Mar 27-31January 21, 2011-CDD will be presenting at the Spring 2011 ACS meeting in Anaheim, CA on March 27-31. Dr. Barry Bunin will be giving a talk entitled “Six Years of Collaborative Drug Discovery in the Cloud.” DIVISION: CINF: Division of Chemical Information SESSION: Integration of Combinatorial Chemistry with Cheminformatics: Current Trends and Future Directions in Drug Discovery [...]
SBS 17th Annual Conference and Exhibition, Mar 27-31January 21, 2011-CDD will be at the SBS 17th Annual Conference and Exhibition in Orlando, FL on March 27-31. Kellan Gregory of CDD will be speaking on behalf of Barry Bunin, PhD in the “Molecular Discovery in Non-traditional, Neglected and Rare Diseases” session. Stay tuned for more details!
Biochemistry Colloquium Seminar @ University of Arizona, Feb 25January 21, 2011-Dr. Sean Ekins will be speaking at the Biochemistry Colloquium Seminar for the Department of Chemistry & Biochemistry at the University of Arizona on February 25. Talk Title: Accelerating Collaborations To Derive in Silico HumanTransporter Models Location/Time: Family and Consumer Sciences 101 at 12:00 PM Host: Florence Tama
NM4TB & MM4TB Meeting, Feb 14-16January 21, 2011-Dr. Sean Ekins of CDD will be presenting at the NM4TB & MM4TB meeting in Davos, Switzerland on Feb 14-16.
CDD Extends Gates GrantJanuary 13, 2011-The Bill & Melinda Gates Foundation recently extended its previous grant to CDD to create a novel database to spark collaborative efforts to discover more effective drugs against tuberculosis (TB). Over the past two years, the CDD TB database (CDD TB DB) has integrated the efforts of academic, non-profit, government and corporate laboratories distributed across [...]
CDD at the Keystone TB Symposia, Jan 15-20January 12, 2011-Dr. Sean Ekins of CDD will be at the Keystone Symposia on Tuberculosis at the Fairmont Hotel in Vancouver, BC. Dr. Ekins will be presenting two posters: Poster 150 “Collaborative Drug Discovery: A platform for transforming Tuberculosis R&D and beyond.” Sean Ekins, Krishna Dole, Anna Spektor, Kellan Gregory, David Blondeau, Sylvia Ernst, Moses M. Hohman, and Barry [...]
CDD Vault Update: Show/Hide Projects and Data SetsJanuary 5, 2011-Back from the holiday break and ready to rock. We continue to focus our efforts on projects, but have decided to make some small tweaks to existing features along the way. Show/Hide projects and data sets Inundated with projects from way back when? Keep active projects in the sidebar and hide the rest. Use the [...]
CDD Vault Update: Saved Searches and Messages for ProjectsDecember 17, 2010-A few more tweaks before enjoying the holidays. Based on feedback and potential IP concerns, saved searches are now project specific at the vault level. Click the “save this search” link on the search page, type in a name and select a project. When posting a message, the list of people you can notify is now updated [...]
CDD Vault Update: Move a Run Between ProjectsDecember 10, 2010-We have been busy enhancing the initial project-related capabilities released on November 19th. Based on your feedback, we also added the following new features: Move a run You can now move a run from one project to another. After clicking on a specific run date, click the Run Details subtab. On the side, click the “Move [...]
Two CDD Board members presenting at Partnering for Cures in NYC on Dec 15thDecember 6, 2010-CDD has always been about Faster Cures. So we are honored that board members Alpheus Bingham and Barry Bunin will be presented at the upcoming Faster Cures meeting “Partnering for Cures” in NYC. Dr. Bingham will be presenting on a panel titled Cloud-Sourcing: Collaboration in a Data-Rich Environment and Dr. Bunin will be presenting on [...]
CRIMMALDI meeting 2010 – Managing the Wealth of New HTS Data for MalariaDecember 1, 2010-In March 2010 CDD participated in a meeting organized by CRIMMALDI held in Liverpool, to discuss how to manage the wealth of high throughput screening for malaria. In particular the focus was how to manage and filter the tens of thousands of expected hits. The final report from the meeting is now available online for [...]
CDD Featured in Bio-IT WorldNovember 30, 2010-CDD was recently featured in the article “Changing the Game of Collaborative Drug Discovery” in the Bio-IT World magazine. Kevin Davies of Bio-IT World showcases CDD’s efforts to bring down the walls within the drug discovery ecosystem using the cloud, as well as our work with the Gates Foundation and Tuberculosis. Read the full text here!
Partnering for Cures, Dec 14-15November 29, 2010-CDD CEO Barry Bunin, PhD, as well as CDD Board Member Alpheus Bingham, PhD, will be presenting on a Panel at the Partnering for Cures conference at the Grand Hyatt in New York City on December 14-15. Here is the abstract and speakers from the titled Cloud-Sourcing: Collaboration in a Data-Rich Environment panel: “The medical [...]
CDD Featured on the Cover of MedChemCommNovember 26, 2010-Dr. Sean Ekins of CDD, along with Dr. Antony Williams of ChemSpider recently published a paper entitled “Meta-analysis of molecular property patterns and filtering of public datasets of antimalarial “hits” and drugs” in Issue 5 of MedChemComm. The article is featured on the front page of the issue. Read the article here, and take a [...]
CDD Vault Update: Manage Projects PageNovember 25, 2010-We performed some minor cleanup tasks and added help messages to the Manage Projects page and the search results. You can again see public data set descriptions by clicking on the “More…” link in the sidebar.
CDD Vault Update: Project-Based CollaborationNovember 19, 2010-… and we’re back! We’ve spent the last three months building projects, the next generation of CDD Collaborate. Introduction We built projects to help you do the following kinds of things: Collaborate on live data: Colleagues at another institution will be running followup studies on your hit list, and you’d like them to upload the [...]
New White Paper: “Collaborative Drug Discovery: The Rising Importance of Rare And Neglected Diseases”November 19, 2010-Dr. Sean Ekins has written a new white paper that merges a summary of our recent publications and some of the topics discussed at the recent CDD community meeting on rare and neglected diseases. You can read the white paper here. We hope it raises even more interest in the work done in the rare and neglected disease community [...]
Reflections on the CDD Community Meeting – Guest Blog by Dr. Michael PollastriNovember 9, 2010-Michael Pollastri, PhD, is an Associate Professor of Chemistry & Chemical Biology at Northeastern University. To read a summary of this year’s CDD Community meeting, click here. I had the distinct pleasure to speak at this year’s Collaborative Drug Discovery User Group and Community Meeting in San Francisco three weeks ago. Since then, I’ve had [...]
CDD-Pfizer Paper On the Cover of Drug Metabolism & Disposition, November 2010 IssueNovember 4, 2010-In August, CDD published two papers in collaboration with Pfizer: “Using Open Source Computational Tools For Predicting Human Metabolic Stability and Additional ADME/Tox Properties” (E-pub ahead of print in Drug Metabolism & Disposition) and “Chemical Space: Missing Pieces in Cheminformatics” (E-pub ahead of print in Pharmaceutical Research). Both papers are now in print, with Figure [...]
CDD Hosts Inspiring 4th Annual UCSF Community MeetingOctober 26, 2010-This past Thursday, on the 21st of October, CDD hosted the 4th Annual CDD-UCSF Community Meeting on “Catalyzing Drug Discovery Research” at the Mission Bay Conference Center in San Francisco. More than 200 registrants signed up to participate. With a diverse group of eight speakers and panelists, the meeting explored the challenges drug discovery faces [...]
4th Annual CDD Community Meeting for Catalyzing Drug Discovery Research!September 30, 2010-The 4th Annual CDD Community Meeting, is a 1-day event on October 21st. The CDD Community Meeting is the best place for the CDD community and all scientists to get together, discuss their research projects, and showcase their work to others in the community. Confirmed Speakers: G. Steven Burrill, CEO, Burrill & Company: Life Sciences [...]
Novartis Shares TB Data on CDD!September 17, 2010-Novartis has made 283 compounds publicly available to the community. This is the first time a big pharma has released data on anti-tuberculosis compounds. Read more about the dataset and register here!
Recent Papers in Press From CDD and Collaborators including Pfizer on Open ModelsSeptember 14, 2010-Hot on the heels of our presentations and posters at the ACS meeting in Boston, we now have several papers in press that detail research conducted with collaborators. These cover topics as diverse as large dataset analysis for Tuberculosis and malaria research, ADME/Tox modeling with open source technologies and some thoughts on what may be [...]
CDD Vault Update: Enhanced Data Normalization and VisualizationAugust 20, 2010-This release completes (for now) our effort to streamline data quality control and analysis. We’ve enhanced data normalization and visualization capabilities, as well as tweaked the final step of the workflow for importing data. Because this release contains a lot of functionality, a short narrative will facilitate our run-through of the new features. Visual Quality [...]
CDD Presents Two Talks & Two Posters at ACS Fall 2010August 20, 2010-CDD will be at the American Chemical Society Fall 2010 meeting from Aug 22-26 at the Boston Convention & Exposition Center. Dr. Sean Ekins will be giving two talks: “Collaborative Drug Discovery: A Platform for transforming neglected disease R&D and beyond” DIVISION: BMGT: Division of Business Development and Management SESSION: Open-Source Drug Discovery SESSION START [...]
Chem Outsourcing Meeting, Sept 14-16August 1, 2010-CDD will be at the Chem Outsourcing Meeting at the Ocean Place Resort in Long Branch, NJ from September 14-16. Kellan Gregory will be on a panel in Track C entitled “Sharing Data Securely & Efficiently in Collaborations with CROs” on Thursday September 16 at 1:15 PM.
Medicines for Neglected Disease Workshop, Sept 10-11August 1, 2010-CDD will be present at the Medicines for Neglected Disease Workshop, to be held at Boston University from September 10-11. Barry Bunin, PhD, will be speaking on applying the CDD Platform to accelerate Neglected Disease R&D.
CDD Vault Update: Automatically Calculate Average ValuesJune 30, 2010-With this release, you can now automatically calculate average values for all data you import into CDD. This is helpful if you perform replicate measurements but typically only want to search and view the average of these replicates. We have also significantly expanded outliers functionality to allow you to flag any readout as an outlier, [...]
CDD Invites Scientists to Join Free Public Data Collaboration ProjectJune 16, 2010-Here at CDD we want to help researchers interested in archiving and publishing their data for the greater good of the community. We were struck in two ways by the surge of interest in GlaxoSmithKline’s recent publication of malaria drug screening data on CDD (see our earlier post for details). First, it’s clear that public [...]
GSK and Online Communities Create Unique Alliance to Stimulate Open Source Drug Discovery for MalariaMay 20, 2010-GSK becomes first company to freely share chemical structures on 13,500 molecules from its compound library Alliances formed with leading scientific research communities from private industry and public-domain data provider BURLINGAME, Calif. May 19, 2010 — GlaxoSmithKline (GSK) had teamed up with leading public-domain data providers European Bioinformatics Institute (EMBL-EBI), the U.S. National Library of Medicine [...]
CDD Vault Update: Structure Masking and Biologist User RolesMay 19, 2010-In a common scenario encountered by our users, chemical libraries for a project have already been imported, and the individuals who are screening compounds do not want to accidentally add or modify molecules. In another related scenario, some of our users want to allow access to their vaults without disclosing any chemical structures. This release [...]
Pharma Giant GSK Openly Sharing Malaria Chemical and Biological Screening DataMay 19, 2010-Guest Blog from Dr. Sylvia Ernst (CDD Senior Director, Community Growth) What would make a publicly traded large Pharma company open up their treasure chest of internal well protected secret screening data and make them available to the world? “Ha! – Nothing!” or “Never!”, you might say… Well – buckle up – the world of [...]
CDD @ BioConference LiveMay 10, 2010-Attending conferences is an important part of any company’s external facing marketing. At CDD we pride ourselves on attending conferences that not only benefit us, but also where we can make an impact. Conferences that focus on the advances and future of integrating life sciences research and technology are of particular interest to us. And [...]
CDD Mentioned in The ScientistMay 7, 2010-The Scientist published an article last week in their digital upgrade section about ELN solutions for laboratories. CDD Community member Robert Damoiseaux is quoted in the article, saying “Your biggest enemy when you have a laboratory is the turnover of postdocs. The postdoc is gone, where the heck is the data?” CDD itself is listed as [...]
CDD Mentioned in the Wall Street JournalApril 29, 2010-Collaborative Drug Discovery was mentioned in an article in the Wall Street Journal: Bill Gates Takes Stake in Creating New Drugs
Accelrys-Symyx Merger: We Welcome the Churn!April 27, 2010- The recent merger between two of the largest players in the narrow preclinical drug discovery informatics space (Symyx and Accelrys) makes it timely to comment on merger and post merger opportunities and impacts: The cost of developing and supporting traditional technologies (especially outside of the cloud where they must be deployed, updated, supported- and [...]
Congratulations to ChemSpider!April 22, 2010-Today, Bio-IT World announced the winners of the sixth Best Practices Awards program. We would like to congratulate Tony Williams and the Royal Society of Chemistry for winning the competition’s first Community Service Prize recognizing excellence in open source, which was awarded for ChemSpider. We are proud to provide links from CDD to ChemSpider for [...]
CDD Vault Update: Faster Scatterplots and Data ImportApril 9, 2010-This release primarily provides performance improvements when loading scatterplots and importing data into your Vault. We also made a number of behind-the-scenes improvements that will help us manage and support our growing user base better. Finally, we fixed several bugs discovered from the previous release. We have increased the maximum number of unique structures that [...]
CDD Celebrates Six Years in the CloudApril 1, 2010-CDD celebrates six years in the cloud today, April 1 2010 (no, not an April Fool’s joke) with the announcement that Andrea Barry is joining our team as the Senior Director of Business Development. For more information, read the full press release about Andrea coming on board here.
CDD Welcomes Andrea Barry as Senior Director of Business DevelopmentApril 1, 2010-BURLINGAME, Calif., April 1 /PRNewswire/ — Today, Collaborative Drug Discovery (CDD) brings Andrea Barry on board to spearhead an initiative to expand into the pharmaceuticals market, building on widespread acceptance of CDD’s platform among academic and biotech researchers. Andrea Barry was the Director of North American Sales for SciTegic prior to its merger with Accelrys, [...]
World TB Day 2010 – A Call to ArmsMarch 24, 2010-Today marks World TB day 2010, 128 years to the day Dr. Robert Koch discovered the bacillus M. tuberculosis. A recent WHO report indicated that approximately 1.8 M people died from TB in 2008, while multi-drug resistance was on the rise. The Stop TB Partnership has set a goal to halve TB prevalence and deaths by [...]
Leading TB Researchers to Present New Findings at New York Academy of Sciences SymposiumMarch 16, 2010-Conquering TB: How Genomic Information and Tools Can Lead to New Tuberculosis Therapies that Combat Drug Resistance NEW YORK, March 16, 2010 — Tuberculosis kills nearly 2 million people annually, and kills more adults than malaria, AIDS, and all tropical diseases combined. TB is the cause of one in four avoidable deaths in the Third [...]
Collaborative Innovation in Biomedicine, June 14-16March 12, 2010-CDD will be presenting at the Collaborative Innovation in Biomedicine Conference on June 14-16 at the Sheraton Philadelphia City Center Hotel in Philadelphia. Sean Ekins of CDD will be giving a talk entitled “Reaching Out to Collaborators on the Cloud: Crowd-Sourcing for Pharmaceutical Research”
SBMC 2010, June 2-6March 12, 2010-CDD will be at the 3rd Conference on the Systems Biology of Mammalian Cells (SBMC) at the Konzerthaus in Freiburg, Germany. Sean Ekins, PhD will be giving a presentation entitled “Toxicity Pathways and Models: Mining for potential off-target effects.”
BioConference Live, June 2-3March 12, 2010-CDD will be presenting at BioConference Live, an online-only conference on June 2-3. Barry Bunin, PhD, will give a talk entitled “Collaborative Drug Discovery Humanitarian and Commercial Researcher Network Case Studies.” Stay tuned for more details!
QSAR 2010, May 24-28March 12, 2010-CDD will be at QSAR 2010 – 14th International Workshop on Quantitative Structure-Activity Relationships (QSARs) in Environmental and Health Sciences. The meeting will take place on May 24-28 at the Hilton Montréal Bonaventure, in Montréal, Canada. Sean Ekins, PhD, will be giving a presentation entitled “QSAR and Systems biology for toxicity assessment: back to the [...]
MIT Innovation Lab Meeting, May 24-25March 12, 2010-CDD will be presenting at the MIT Innovation Lab Meeting at the Google Campus in Mountain View on May 24-25. CDD CEO Barry Bunin, PhD, and CDD Board Director Alpheus Bingham, PhD will be giving a talk on the pharmaceutial industry ecology and CDD’s novel methods and results in producing open innovation in this space.
2010 Accelrys User Group Meeting, May 4-6March 12, 2010-CDD will be presenting at the 2010 Accelrys User Group Meeting, taking place from May 4 to May 6 in Boston, MA, at the Westin Waterfront Hotel. CDD’s own Sean Ekins, PhD will be giving a talk entitled “A Collaborative Database And Computational Models For Tuberculosis Drug Discovery.”
Drug Discovery Chemistry, Apr 27-28March 12, 2010-CDD will be at the Drug Discovery Chemistry Conference in San Diego on April 27-28. CDD’s Barry Prom will be at the conference, and will use the ASINEX booth as a meeting point. About ASINEX: With more than a sixteen year history, ASINEX is a world leader in supplying compound libraries, focused libraries, custom libraries, [...]
Sage Commons Conference, Apr 23-24March 12, 2010-CDD will be at the Sage Commons Conference in San Francisco on April 23-24. CDD Community Advocate Orion Jankowski, PhD will be attending the meeting.
EurasiaBio 2010, April 13-16March 12, 2010-CDD will be at the EurasiaBio 2010 conference at the World Trade Center in Moscow, Russia. Sean Ekins, PhD will be giving a presentation entitled “Opportunities for Computational Drug Discovery and Screening: Improving Hit Quality and Facilitating Collaborations.”
NYAS TB Meeting, April 6March 12, 2010-CDD is proud to be a marketing partner for the New York Academy of Sciences Tuberculosis Meeting, entitled “Tuberculosis: Novel Therapies Through Knowledge of the Causative Agent.” The event will take place on the 6th of April at the New York Academy of Sciences, as well as over the internet via Webinar. Sean Ekins, PhD and [...]
ACS Spring 2010, March 21-25March 12, 2010-CDD will be presenting two talks, giving a poster, and exhibiting at booth 104 at the Spring 2010 ACS National Meeting and Expo at the Moscone Center in San Francisco, CA. For the Division of Chemical Information, Barry Bunin, PhD will give a talk: TITLE: “Five Years of Drug Discovery in the Cloud” DIVISION: CINF [...]
Crimalddi Workshop, March 17March 12, 2010-Sean Ekins, PhD, of CDD will be at the Crimalddi Workshop in Liverpool, UK on the 17th of March.
Guest Blog: Dr. Jonathan Baell, Medicinal Chemistry Group Leader, CRC for Cancer Therapeutics at WEHIMarch 8, 2010-We at CDD wish to bring attention to useful developments to the community. In this case it was a recently published J. Med. Chem paper brought to our attention by our SAB member Christopher Lipinski titled “New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in [...]
CDD Vault Update: Search Across All Data Sets at OnceMarch 5, 2010-The big story in this release is the new CDD Portal, which allows you to search across all of your CDD Vaults and available data sets at once. Prior to this release, if you had data in multiple vaults, you could only search within each vault individually. This release also includes a much requested smaller [...]
CDD Vault Update: Preparing for ProjectsJanuary 22, 2010-Most of the work for this release was behind-the-scenes restructuring to prepare for the upcoming series of “projects” releases. There were a few user-visible enhancements delivered, however. As of this release, if your data import has errors, you now have the option to commit the import (so that data without errors is added to your [...]
GSK Takes a Leap Towards "Open Innovation" in Neglected Disease ResearchJanuary 21, 2010-Yesterday, GlaxoSmithKline announced a pledge to establish a data collaboration strategy in order to forward neglected disease research. The first initiative is the creation of an “Open Lab,” a data collaboration project that will allow scientists to tap into the wealth of knowledge available to GSK while pursuing their own projects simultaneously. GSK will also [...]
Molecular Medicine Tri-Conference, Feb 3-5January 15, 2010-CDD will be presenting a talk, moderating a panel, and will exhibit at a booth at the Cambridge Healthtech Institute’s Molecular Medicine Tri-Conference in San Francisco, CA on Feb 3-5. Barry Bunin, PhD, CEO of CDD will give a brief talk entitled “Collaborative Drug Discovery Humanitarian and Commercial Researcher Network Case Studies.” He will then moderate [...]
Lab Automation 2010, Jan 23-27January 9, 2010-CDD will be presenting at the 2010 Lab Automation Conference in Palm Springs, CA, taking place from January 23-27. Barry Prom of CDD will be giving a poster entitled titled: “Five Years of Drug Discovery in the Cloud” on Tuesday, January 26 from 13:00 – 15:00, in the Informatics Track.
CDD Thoughts on Data SharingDecember 22, 2009-As we enter the holidays, the season of giving and sharing, we here at CDD reflect on our commitment to broadening precompetitive collaboration and data sharing in the drug discovery ecosystem. We see this as the necessary and sufficient condition for enabling the economics of specialization for both humanitarian and commercial drug discovery. We are [...]
CDD Vault Update: ScatterplotsDecember 18, 2009-The big story this month is the beta release of our new scatterplots module. In addition, you can now specify more detailed run criteria on the Explore Data/Search page, and you can view and delete your mapping templates (for more about mapping templates see the October 2 release below). Scatterplots We are happy to announce the beta [...]
Scatter Plots Are Live on CDD!December 18, 2009-Just in time for the holiday, we are happy to announce the beta release of a much-requested feature addition to CDD Vault: Scatter Plots. Before we delve into details, note that we’ve implemented this feature without requiring the installation of additional plug-ins and in a way that works for all supported browsers (and even some [...]
CDD Vault Update: Export to CSVNovember 25, 2009-Export to CSV This release adds the ability to export any search results in the CSV (Comma Separated Values) format. This is the fastest way to export large amounts of data, and the resulting file can be easily opened with Excel. Your export format preference (XLS, CSV or SDF) is remembered by the application. We [...]
CDD Vault Update: Export dose-response plots to ExcelNovember 20, 2009-This release wraps up a series of releases focused on data import. We have also included a couple highly requested smaller features (the top two below). The next major feature we plan to tackle before the end of the year is scatter plots. Contact support for a preview. Export dose-response plots to Excel We are happy [...]
New Software Release and 3rd Annual Community Meeting Showcase CDD’s Cloud Based Drug Discovery Application Coming of AgeNovember 16, 2009-CDD is proud to announce the release of the third generation of their widely used web-based software platform, aptly dubbed “CDD3”. Anticipating the acceptance of cloud-based collaborative software as an industry standard, CDD has pioneered this field since its first generation software was released five years ago. The new platform focuses on adding novel features [...]
CDD Vault Update: Hydrate supportNovember 10, 2009-Hydrate support (Only for vaults using CDD’s “registration system” module) For each batch we now explicitly record the number of hydrates associated with the given salt of the molecule. This primarily affects batch formula weight calculations. During data import and manual registration, in addition to stripping hydrates from core structures, we now record the number of [...]
CDD Vault Update: Add Prefixes, IUPAC Name Support, Neutralization and MoreOctober 30, 2009-This is a minor release providing several useful new features and a few design and bug fixes. Automatically add prefixes to molecule names, plate names, and batch external identifiers In Data Import Step 2, you can now provide prefixes to prepend to, for example, every molecule name in the file. This is very helpful when [...]
Drug Discovery Partnership: Filling the Pipeline, Oct 28-30October 23, 2009-CDD will be presenting at the Drug Discovery Partnership: Filling the Pipeline conference. The conference takes place October 28-30 at the Hyatt Regency in Boston, MA. Sean Ekins of CDD will be on a panel entitled “Optimizing Integration in Early Stage Drug Discovery,” during Track A of the “Strategic Alliance” theme.
Figon Dutch Medicine Days, Oct 12-14October 7, 2009-CDD will be presenting at the Figon Dutch Medicine Days. The conference takes place October 12-14 at the Congress Hotel De Werelt in Lunteren, in The Netherlands. Sean Ekins of CDD will be giving a talk entitled “Toxicity Pathways and Models: Mining for potential side effects,” at the ASAT Innovation program.
CDD Hosts an Exciting 3rd Annual UCSF Community Meeting on Oct. 1October 7, 2009-Last Thursday, CDD held its 3rd Annual Community Meeting for Catalyzing Humanitarian and Commercial Research, at the J. David Gladstone Institutes at UCSF Mission Bay in San Francisco. With over 180 registrants as well as ten guest speakers and panelists, the event was an eye-opening exposé into the issues facing academics, non-profits, biotechs, and pharmas [...]
CDD Vault Update: Release of CDD3October 2, 2009-This is the first release of CDD3, whose overarching goal is to streamline, simplify and enhance the user experience. Dashboard The dashboard has been completely redesigned to provide you with quick links to the data and tools you access most. In addition to the standard recent activity log, the Recent Activity tab now lists recent protocols and [...]
CDD is Featured in the ACS Chemical & Engineering NewsSeptember 17, 2009-CDD is back in the spotlight, this time in the “Digital Briefs” section of the American Chemical Society’s (ACS) Chemical and Engineering News. The Digital Briefs section explores “New software and websites for the Chemical Enterprise,” so it’s great to see us up there with Reuters’ Endnote and ChemAxon’s JChem software. The article highlights CDD’s [...]
3rd Annual CDD – UCSF Community Meeting, Oct 1September 15, 2009- CDD will be hosting our 3rd Annual Community Meeting for Catalyzing Humanitarian and Commercial Drug Discovery Research on Oct 1, 2009, at the J. David Gladstone Institutes at the UCSF Mission Bay Campus. For more information, click here.
3rd Annual Collaborative Drug Discovery – UCSF Community Meeting for Catalyzing Humanitarian and Commercial Research to be Held October 1stSeptember 15, 2009-SAN FRANCISCO, Sept. 15 /PRNewswire/ — The Gladstone Center for Translational Research and the California Institute for Quantitative Biomedical Research (QB3) at the University of California, San Francisco (UCSF) together with Collaborative Drug Discovery, Inc. (CDD) are pleased to announce the prestigious speakers and panelists that will present at the 3rd Annual Collaborative Drug Discovery [...]
AsisChem to Offer Libraries through CDD!September 11, 2009-On the heels of our announcement with ChemBridge, CDD is announcing a collaboration with AsisChem to provide libraries on CDD’s Public Access Page. Stay tuned for more information on when the libraries are to be uploaded and what molecules they contain…
CDD’s Suite of Products Have New Names!August 18, 2009-We are excited to announce that the CDD database platform is getting a new moniker! In fact, there are three new names to look out for. Why does it matter, why should you care? Good branding, like good product design, is about defining and communicating the essence of a product and its function. Our goal [...]
Gordon Research Conference on Tuberculosis Drug Development, Aug 16-20August 10, 2009-CDD will be presenting at the Gordon Research Conference on Tuberculosis Drug Development. The conference takes place August 16-21 at Magdalen College, Oxford in the UK. Sean Ekins of CDD will be presenting a poster entitled “Collaborative Drug Discovery Tuberculosis Database (CDD TB) and 1D, 2D, and 3D Computational Model Development.”
Drug Discovery and Development Week, August 3-6August 3, 2009-CDD will be presenting at the Drug Discovery & Development Week, hosted by IBC Life Sciences, on August 3-6 at the World Trade Center in Boston, MA. Sean Ekins of CDD will be presenting a poster on “A Collaborative Web-Based Architecture For Sharing ToxCast Data” at the “Drug Safety Strategies to De-Risk Compounds” session.
Pharma Getting on the CloudJune 5, 2009-The American Chemical Society’s Chemical & Engineering News recently published an article about the Pharmaceutical Industry adopting cloud computing technologies. Frustrated with outdated, inefficient storage created through in-house information technology, several large pharma companies are turning to consumer Internet alternatives in database technology. Finally! Cloud Computing has proven successful in a variety of database storage [...]
Hepatotoxicity and Drug Safety Conference, June 10-11June 2, 2009-CDD will be presenting at the 2nd Annual Hepatotoxicity and Drug Safety Conference, hosted by the World Pharmaceutical Congress, June 10-11 at the Loews Philadelphia Hotel in Philadelphia. Sean Ekins of CDD will be presenting a poster on “A Collaborative Web-Based Architecture For Sharing ToxCast Data.”
Drug Discovery: Easing the Chemistry Bottleneck, June 8-9June 2, 2009-CDD will be presenting at Drug Discovery: Easing the Chemistry Bottleneck, hosted by Opal Events, June 8-9 at the Pennsylvania Convention Center in Philadelphia. Sean Ekins of CDD will be giving a talk entitled “Computational Drug Discovery: Integrating a Collaborative Database.”
6 New Data Sets Available for Public Access Use!May 22, 2009-In the last month, we at CDD have released six new Data Sets on our Public Access Page! Three of these Data Sets are from TimTec, a chemical vendor we have collaborated with before. The first new TimTec library is their Diversity Set, a screening library of about 10,000 diverse compounds. Second is a set [...]
Future of Big Pharma Collaboration: The Pistoia AllianceMay 15, 2009-Here at CDD, we’ve acknowledged the importance of collaboration in advancing drug discovery research. While our software can function as a stand-alone database for archiving and mining public data, researchers have the ability to take their work to the next level and selectively collaborate with their peers. Around the globe, the idea of collaboration in [...]
Microsoft Life Science Division Tweets about CDD Presentation!May 4, 2009-CDD has joined the fray of Web 2.0 on-the-go! Last week, Barry Bunin, PhD (our CDD CEO) gave a presentation at the Bio-IT conference in Boston. Les Jordan of the Microsoft Life Sciences division, while sitting in the audience, posted a tweet about Barry’s talk, even providing a link to our website. With the Twitter [...]
Thursday’s Network OutageApril 13, 2009-Many of you noticed that CDD was unavailable for much of the day on Thursday, April 9th. We wanted to take a moment to explain in more detail the events that caused this outage, and to alert you to a new resource, http://status.collaborativedrug.com. Those of you who live in the San Francisco bay area might [...]
We Must Stop Tuberculosis At All Costs – Acknowledge the Efforts on TB DayMarch 20, 2009-Tuberculosis (TB) has not only scarred lungs, it has scarred memories, families, communities, countries and, ultimately, it has scarred the world. If you are sitting in front of a computer anywhere in the Western World, and were born after World War II it is highly probable that you are scarred too..this time as a result [...]
Join us on Our LinkedIn GroupMarch 16, 2009-LinkedIn has become one of the primary sites on the web for people to connect, network, recommend each other and, for our needs, host discussions within a Group of interested parties who care about what Collaborative Drug Discovery is all about. Over the next few months we will be holding some interesting discussions inside the [...]
Bio-IT World Conference and Expo, April 27-29March 13, 2009-CDD and ChemZoo are both presenting at the Bio-IT World Conference and Expo, April 27 to 29 at the World Trade Center in Boston. Antony Williams of ChemZoo will present in Track 4: Computational Chemistry on “Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry.” Barry Bunin of CDD will present in Track 1: [...]
Drug Discovery for Protozoan Parasites, March 23March 13, 2009-CDD will give a poster at the upcoming Keystone Symposia Conference on Drug Discovery for Protozoan Parasites. Poster Title: Community-Based Neglected Infectious Disease: Collaborative Drug Discovery Case Studies Authors: B Bunin, M Hohman, S Ernst, K Gregory Session: Poster Session 1, #112 When: Monday, March 23, 2009 Location: Beaver Run Resort, Breckenridge, Colorado.
ACS – Salt Lake City, March 22March 13, 2009-Barry A. Bunin, PhD will present a paper titled “”Community-based small molecule collaborative drug discovery for neglected infectious diseases and cancer” at the upcoming Spring 2009 ACS meeting in Salt Lake City, Utah. Session information is as follows: PAPER TITLE: “Community-based small molecule collaborative drug discovery for neglected infectious diseases and cancer” DIVISION: Division of [...]
For The TB Community, CDD Software Is Free, Gratis, No ChargeFebruary 16, 2009-Dear CDD Community, Due to the overwhelming response and interest in the CDD platform and services for the Tuberculosis R&D Community following our announcement with the Bill & Melinda Gates Foundation and presentations at the Keystone Tuberculosis conference, we are excited to inform you that we have made a major change to our policy and [...]
CDD’s Tuberculosis Effort Covered by BioInform and Drug Discovery NewsJanuary 29, 2009-Two articles were recently published covering CDD’s new effort for the tuberculosis research community and our collaboration with TBDB. To read more, see Bioinform’s article, “Collaborative Drug Discovery to Use Gates Foundation Grant for Tuberculosis Database”, and the article in Drug Discovery News, “Tuberculosis portal”. Important note regarding BioInform: Reading the BioInform article once straight [...]
Drug Discovery News Acknowledges Our EffortsJanuary 28, 2009-In an ongoing flurry of recognition of our efforts to support the discovery of new cures for Tuberculosis, and our related funding from the Bill and Melinda Gates Foundation (as announced here) the Informatics arm of the Drug Discovery News web portal has acknowledged our work. They interviewed Ken Duncan, a senior program officer at [...]
New Release: Customize Mine ResultsJanuary 24, 2009-Last evening we released the latest update to CDD, customizable mine results. This release makes it easy to add (or remove) protocols, readouts, molecule synonyms and/or user-defined fields to/from your mine results, allowing you to customize the displayed data to be most relevant. To access this new feature, perform a mine query, then click the [...]
Distributed Drug DiscoveryJanuary 22, 2009-In the inaugural issue of Volume 11 of the Journal of Combinatorial Chemistry Anthony Czarnik commented on the concept of Distributed Drug Discovery, D3. This concept was introduced in papers in that issue by Profs William Scott and Martin O’Donnell of the IUPUI (Indiana University-Purdue University Indianapolis). The three papers are: Distributed Drug Discovery, Part [...]
Molecular Medicine Tri-Conference: San Francisco, CAJanuary 5, 2009-Barry A. Bunin, PhD will be presenting a talk titled “Leveraging Web 2.0 Social Networks for Collaborative Drug Discovery” at the Molecular Medicine Tri-Conference at the Moscone Center in San Francisco, CA. The presentation will be in the Executive Summit On Strategy and Innovation Track to kick off the section titled DEVELOPING NEW PARTNER/ALLIANCE/COLLABORATION MODELS. [...]
CDD is moving officesDecember 29, 2008-CDD is in a stage of growth, and we will be relocating our offices over the holiday period and opening our doors at a new location. Update your contact details with this new address: 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010. Come and visit with us a while and discuss our efforts to build [...]
New Release: Archive ReferencesDecember 29, 2008-We’re happy to announce the release of the latest version of CDD’s software, now available live at www.collaborativedrug.com. The big update in this release is the ability to archive information on scientific references (references as in the references section of a publication). There are two goals for this functionality: 1) to allow researchers to share [...]
Keystone Symposium on Tuberculosis: Biology, Pathology and TherapyDecember 24, 2008-CDD will present a poster and give a talk at the Keystone Symposium on “Tuberculosis: Biology, Pathology and Therapy”, to be held in Keystone, Colorado from January 25th through the 30th. Poster: A New, Collaborative, Web-based Database for the Tuberculosis Research Community Authors: S Ekins; M Hohman; B Bunin Session: Poster Session 2 Poster Number: [...]
Assembling Datasets for the Users of the CDD PlatformDecember 19, 2008-The number of contributers and datasets on the Collaborative Drug Discovery platform is increasing on an ongoing basis. Not only are our users adding to the content, both public and private but we ourselves continue to assemble databases to benefit the community. Most of our efforts will result in an increase in the Public Access [...]
Collaborative Drug Discovery Walks the Web to ChemSpiderDecember 12, 2008-We are all about Collaboration…it’s in our name! Since our databases sit on a growing foundation of small molecules and their potential contributions to drug discovery, it is natural that we would want to connect our structure collection to additional information that could be of value to our users. There are many open resources of [...]
Collaborative Drug Discovery Moving Soon…And Hiring NowDecember 10, 2008-How many ways are there to communicate how something small can grow to become something much bigger… Every long journey starts with a single step Large Oaks from little acorns do grow And maybe one for our era… Today the financial sector, tomorrow the auto industry and next week ? Well, let’s go with the [...]
ASTMH 2008 Annual Meeting in New OrleansDecember 3, 2008-CDD will be at the American Society of Tropical Health and Hygiene (ASTMH) 2008 Annual Meeting in New Orleans next week. CDD President Barry Bunin will present a poster: Poster Title: 4 Community-Based Neglected Infectious Disease Collaborative Drug Discovery Case Studies Presentation Number: 180 Poster Session A Monday, December 8, 2008 Noon – 1:30 pm [...]
Public Access vs. Commercial AccessNovember 26, 2008-CDD has done some things a bit unusual for a commercial entity. We have focused initially on neglected infectious diseases that asymmetrically impact the poorest people in the world, and we have worked with a community of leading scientists to aggregate what we believe to be the most relevant information for drug discovery researchers in [...]
Welcome to the Collaborative Drug Discovery BlogNovember 17, 2008-Welcome to the Collaborative Drug Discovery Blog. Why a blog now especially since CDD has been around for a couple of years and working hard on providing an environment for drug discovery scientists to collaborate? There is a lot going on here and based on feedback from some of our users and the way we [...]
Second Annual CDD Community MeetingOctober 7, 2008-The 2nd CDD Community Meeting was wildly successful with 176 registrants and 20 Posters. The symposium speakers presented on important research and collaboration around neglected diseases and orphan drugs. The Keynote presentation by J. Leighton Read of Alloy Ventures provided crucial insight into how pre-clinical research affects clinical drug development. The Discussion Panels featured members [...]
Meet CDD at these Upcoming ConferencesJune 5, 2008-CDD will be attending several conferences in the second half of this year. If you would like to meet with us while at any of these conferences, please contact us at info@collaborativedrug.com to schedule a time.
Drug Discovery News Article on CDDDecember 1, 2007-Drug Discovery news has published an article on CDD’s work with the St. Jude Children’s Research Hospital. From the article: A collaboration to identify and develop drugs for resistant strains of malaria draws on an unusual combination of resources: U.S. Army research from 1946 plus 21st century informatics and lab technology. The joint work on [...]
Collaboration and Security ReleaseOctober 26, 2007-CDD updated our core database software today with the initial release of our collaboration technology and a number of security updates. Some of the highlights of the release: Community data, including the list of FDA approved drug structures, is now available to all users. Over 27 separate security enhancements to make sure that your data [...]
Free Access to Literature Data on Chagas’ Disease Offered OnlineOctober 17, 2007-Collaborative Drug Discovery has captured extensive literature data from six years of recent publications focused on the fight against Chagas’ disease. Now, for the first time, these data are available to researchers free of charge, via the CDD Database. Sources include the Journal of Medicinal Chemistry, Bioorganic & Medicinal Chemistry, the Journal of American Chemical [...]
Army Malaria Data Released to the CDD CommunityOctober 11, 2007-Collaborative Drug Discovery, Inc. (CDD, Inc.) and St. Jude Children’s Research Hospital have joined together for a project aimed at speeding the development of new drugs to overcome resistant strains of malaria. The collaboration combines the malaria drug data and informatics technology of CDD with the drug discovery expertise of the St. Jude Department of [...]
Collaborative Drug Discovery Releases Next Generation Database for Both Private Collaborations and Public Open AccessJuly 5, 2007-Collaborative Drug Discovery (CDD, Inc) is pleased to announce the introduction of its next generation database technology. Collaborative Drug Discovery’s Web-based database enables scientists to collaborate in novel, global efforts to more effectively develop new drug candidates for commercial and humanitarian markets. The technology enables novel community-based research efforts that become more and more useful [...]
First Annual CDD Community MeetingMarch 5, 2007-The meeting provided new perspectives on collaborative research, scientific community development and global health, with a focus on infectious diseases of the developing world. We had 114 people register, 10 posters presented and many great speakers. Presentation Videos and Slides (PDF) Developing drugs for neglected parasitic diseases in an academic incubator James McKerrow, PhD, Sandler [...]
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Human vs. Machine-Enhanced Scientific Discovery – CDD Webinar Video September 27, 2016 - We’re delighted to share with you the video from our exciting recent “Human vs Machine-Enhanced Scientific Discovery” Webinar: The panelists peered into a rapidly approaching future world where computers are doing experiments side-by-side with scientists. In that reality, having data that is FAIR (Findable, Accessible, Interoperable, and Reusable) is critical. The panelists reframed the way we [...]
CDD Vault Powers Virtual Pharma Distributed Drug Discovery September 22, 2016 - Dr. Mike Pollastri spent almost a decade as a research scientist in Big Pharma (Pfizer) before turning to academia and today he is running one of the best known neglected disease research labs at Northeastern University. Mike generously is sharing this slide set which he presented at the 250th meeting of the ACS 2015 so that others who think they can not afford to run drug discovery consider this economical distributed, virtual model....
CDD Vault Update: Cancel Export September 9, 2016 - Today's release brings several usability enhancements to help you get data in to and out of your vault smoothly. Notably, we added an option to cancel an export, added support for European date formats, and made a couple of additions to the API.
Spotlight Interview with Dr. Andrew Calabrese – VP of Chemistry at AgriMetis September 6, 2016 - Going from academic research to industrial research, came with the realization that bulk data drives industrial research, whether its pharmaceuticals or agrochemicals. In academia you might focus in on a very specific issue and track data very carefully, on individual data points. In industry it's all about bulk data, and it's about drawing plots of multiple compounds vs multiple data points, and trying to find correlations and find the outliers and find the reason why compounds are doing what they're doing. CDD Vault is a great tool for bulk data analysis...
CDD to Present and Exhibit at the 14th Annual Discovery on Target in Boston (September 19-22) August 29, 2016 - CDD will be presenting scientific talks and exhibiting at the upcoming Discovery on Target conference in Boston, between September 19th and 22nd, 2016. Come visit us in Booth 42 CDD will be exhibiting the latest developments in our hosted solution for chemical registration, bioassay data management, Structure Activity Relationship (SAR) analysis, calculations, inventory, and visualization [...]
CDD Vault Update: Software Upgrade Part 2 August 19, 2016 - Today's release brings another major upgrade to the software stack that CDD Vault runs on. This allows us to maintain good application security and paves the way for upcoming features. It was a massive amount of work, but if we did everything right you won't notice a difference. In addition we increased performance and introduced several small enhancements.
BioAssay Express (a bit of an unveil) August 4, 2016 - CDD's BioAssay Express software allows you to convert human readable bioassays into machine readable, marked up text. The technology has been tested on over 3000 "best of Pubchem" MLPCN assays. New insights and patterns can be seen around the widely shared "probe" compounds to further validate the utility of the approach. With the Common Assay Template, we've tried to make good subjective calls regarding the most important parameters influencing bioassays, whilst keeping a minimum number of categories. However, it is worth emphasizing that the underlying technology can be used with any templates, terms, and ontologies (i.e. yours). As a matter of focus, we've focused this new technology on bioassays. In contrast to our polished, professional CDD Vault platform, Bioassay Express is still a relatively new technology, yet clearly it does work. For those interested in collaborations or evaluations please send an email to info@collaborativedrug.com if you'd like to try using this technology with your own protocols (behind firewall, online in Bioassay Express, or potentially integrated with CDD Vault)...
Share Your Delight With CDD While Helping Fund Neglected Disease R&D July 12, 2016 - CDD has teamed up with David Swinney’s colleagues at iRND3 and you to introduce a CDD Vault Referral Program that simultaneously raises money for their non-Profit Neglected Disease Research. The Institute for Rare and Neglected Diseases Drug Discovery (iRND3) is not only a partner for our referral program, they are also a very active CDD [...]
Top Ten Reasons Academic Research Laboratories Need CDD Vault July 12, 2016 - Top Ten Reasons Academic Research Laboratories Need CDD Vault
Students come and go, but data live on
Students learn about data management and analysis tools
Management of research workflow is enhanced
Graduates’ job prospects are enhanced
Chemistry and Biology students learn about cross-disciplinary teams
Structure-activity analyses are enhanced
Research collaborations are promoted
New Leads and other IP values are enhanced
Students and researchers can focus on science, not maintaining datasystems
Affordable, budgeted cost instead of expensive in-house datasystems
GSK’s Kinetoplastid Research Data Set Available FREE Within CDD Vault July 12, 2016 - In an effort to fuel open-source research and drug discovery in Kinetoplastid diseases, GSK Tres Cantos and CDD have assembled three Kineto Boxes containing 592 New Small Molecules. Using parallel whole-cell phenotypic assays, the GSK HTS diversity set of 1.8 million compounds was screened against the three kinetoplastids most relevant to human disease, i.e. Leishmania [...]
Genentech & UCSF Library Selection – CDD Webinar Video June 1, 2016 - CDD’s May Town Hall Webinar explored how the selection of optimal chemical libraries can improve the drug discovery process. Guided by a distinguished panel of speakers, this Town Hall style webinar challenged our panelists, as well as the audience, to think hard about what should be included in an optimal small molecule library and to [...]
CDD to Present at the World Preclinical Congress – Mastering Medicinal Chemistry Conference in Boston (June 15-17) May 25, 2016 - CDD will be presenting scientific talks, posters and exhibiting at the upcoming World Preclinical Congress Mastering Medicinal Chemistry conference in Boston, between June 15th and 17th, 2016. Anna Spektor, CDD’s Customer Success Manager, and Shirley Louise-May, CDD Advocate, will be presenting a talk and 2 posters: “CDD Vault: Activity, Registration, Visualization, Collaboration” “CDD Vision: A [...]
CDD TOWN HALL WEBINAR VIDEO: DRUG DISCOVERY PUBLIC-PRIVATE PARTNERSHIPS (PPPs) April 19, 2016 - CDD’s inaugural CDD Town Hall Webinar explored how Public-Private Partnerships (PPPs) have inspired efforts to improve the pace of drug discovery. Guided by a distinguished panel of speakers, this Town Hall style webinar examined: Various approaches for establishing successful PPPs How PPPs have affected the drug discovery efforts for Commercial and Neglected Tropical Diseases The [...]
CDD Vault Update: Design Refresh April 14, 2016 - This release provides a visual refresh to CDD Vault, plus navigational cleanup and simplification. Design The new design greets you on the log-in page, and is applied throughout the site. We’ll let it speak for itself, but we hope you like it as much as we do. New Settings Page All settings have been consolidated [...]
CDD Spotlight Interview with James Moe – President, CEO and a co-founder of Oligomerix April 14, 2016 - “We’re using CDD Vault as a way of storing our chemical structures, as a way of searching them, as a way of storing all of our assay data. We’re also using it for doing calculations, for analyzing our data, for creating reports and communicating the data to others, and then also, very importantly, for working [...]
Celebrating A Dozen Years of Collaborative Drug Discovery in CDD Vault: 12 Popular Posts April 6, 2016 - To commemorate a dozen years of trusted, secure data hosting by leading drug discovery project teams in CDD Vault, we're sharing a dozen popular recent posts:
1. Why using pIC50 instead of IC50 will change your life (9304 Views - 14 July 2014). Video posted on Apr 15 2015: https://www.collaborativedrug.com/buzz/2015/04/15/on-demand-video-from-the-pic50-scientific-webinar/
2. New Data from the FDA Available for Public Access Use (1504 Views - 30 April 2011)
3. New White Paper: Promoting Effective Project Teams for Drug Discovery (1492 Views - August 6 2015)
4. CDD First Live Webinar Event - Are Your Compounds Biased by Your Discovery Techniques (with Christopher Lipinski and Matthew Soellner...
CDD Spring Tour – ADDC, EB, ASPET, BioIT, UCSD, PPP March 18, 2016 - “Spring is the time of plans and projects.” -Leo Tolstoy In Anna Karenina, Leo Tolstoy wrote that “Spring is the time of plans and projects.” How Leo knew of CDD Vault’s collaborative Project design is beyond us, but he was correct in asserting that Spring is the time to plan on joining CDD as we [...]
Valuable New ASINEX Libraries Now in CDD Vault March 10, 2016 - How can your early drug discovery program be more efficient? Have you ever screened ASINEX compounds? Did you know you can view ASINEX, and other leading vendor, libraries directly in CDD Vault? CDD has a long-standing partnership with ASINEX going back more than 10 years. Together we provide innovative offerings for drug discovery scientists that [...]
Seminar: Lunchtime with Collaborative Drug Discovery March 9, 2016 - Join us for a lunchtime seminar at the University of California in San Diego (UCSD) Wednesday, April 6, 2016 10:00 am – 2:00 pm PT Register for and join our free seminar to learn how local researchers are applying research informatics to their chemical and biological experiments. You will learn about chemical registration, data archival, [...]
CDD to Attend the Academic Drug Discovery (ADDC) UK Workshop 2016 (March 22nd – 23rd, 2016) March 7, 2016 - CDD will be attending the upcoming Academic Drug Discovery (ADDC) UK Workshop at the Cripps Court Magdalene College in Cambridge, United Kingdom, on March 22nd & 23rd, 2016. CDD will be available to discuss the latest developments in CDD Vault, our hosted solution for chemical registration, bioassay data management, Structure Activity Relationship (SAR) analysis, calculations, [...]
CDD Vault Update: Introducing New Inventory for CDD Vault February 27, 2016 - Have you ever gone to the storage freezer to get a stock compound, only to discover that the vial is empty? Assuming you found the vial at all? Or have you spent the afternoon trying to track down a compound, wondering to yourself if there’s an app for that? And if you work in the [...]
CDD Town Hall Webinar: Public-Private Partnerships (PPPs) for Drug Discovery February 24, 2016 - SAVE THE DATE for CDD’s inaugural Town Hall: What are Public-Private Partnerships for Drug Discovery? In recent decades, the proliferation of world-wide epidemics and health emergencies (such as HIV, MERS, Ebola, and most recently Zika) has inspired efforts to improve the pace of drug discovery through large-scale collaborations. So-called Public-Private Partnerships (PPPs) have been [...]
CDD to Present at 3rd Annual Medicinal Chemistry Strategy Round Table Meeting in the United Kingdom (9th March, 2016) February 23, 2016 - CDD will be speaking in and facilitating interactive and informal discussions at the upcoming Medicinal Chemistry Strategy Meeting in the United Kingdom, on March 9th, 2016. CDD will also be available to discuss the latest developments in CDD Vault, our hosted solution for chemical registration, bioassay data management, Structure Activity Relationship (SAR) analysis, calculations, and [...]
CDD to Present at 251st American Chemical Society National Meeting & Exposition in San Diego (March 13-17) February 19, 2016 - CDD's CEO (Dr. Barry Bunin) and CSO (Dr. Sean Ekins) will present at the 251st ACS National Meeting in San Diego March 13-17, 2016:
PAPER ID: 2414195
PAPER TITLE: “CDD Vault: successful product case study”
DIVISION: SCHB
SESSION TYPE: Oral...
CDRD Chooses CDD for New Drug Discovery Informatics Platform February 11, 2016 - Press release BURLINGAME, CA and VANCOUVER, BC (February 11, 2016) — Collaborative Drug Discovery (CDD) today announced that The Centre for Drug Research and Development (CDRD) has chosen CDD Vault to replace their Drug Discovery Informatics Platform. After in-depth evaluation of leading systems, CDRD decided on the CDD Vault platform. CDD Vault is a hosted [...]
How can the collaborative scientific community be proactive and more agile – not just for Zika virus, but also for the next epidemic around the bend? February 5, 2016 - From the desks of Sean Ekins, CSO and Barry Bunin, CEO
You would have to be hiding under a rock to have not heard about the Zika virus which is being found in the Americas and spreading globally as people travel. The Zika virus, carried by one of humanity’s long-term pests the mosquito, so far appears to be capable of being sexually transmitted, as well as transmitted with blood transfusions and by birth. It has also recently been found in urine and saliva. There have been large numbers of children born with microcephaly which has been associated with the virus though this is not firm since causality has not been proven, yet the correlative relationship appears strong. We currently cannot predict what scientific discovery or epidemiological finding will be made next or how this will unfold.
It is pretty clear... 
CDD Super Bowl Sunday February 1, 2016 - As the Super Bowl marches into CDD's backyard, we also have an internal competition heating up.
This has nothing to do with the performance of the Broncos, Panthers, Cardinals, or Patriots - but rather the fierce competition of prioritizing informatics functionality to expedite drug discovery research.
In the Eastern Conference, Visualization-Calculations matched up against Inventory needs.
And in the Western Conference, it was...
Top Ten Reasons for Biotechs to Acquire CDD Vault January 12, 2016 - Top Ten Reasons for Biotechs to Acquire CDD Vault Scientists may come and go, but data live on Encourage project scientists to follow healthy data management practices Enhance research workflows Improve acquisition and analysis of project data Serve all members of the project team Promote research collaborations Enhance structure-activity analyses Protect New Leads and other [...]
CDD to Present at SLAS 2016 National Meeting in San Diego (Jan 25-27) January 5, 2016 - CDD will be presenting three scientific talks at the upcoming Society for Laboratory Automation and Screening (SLAS) Conference in San Diego, between January 25th and 27th, 2016. Dr. Sean Ekins, CSO at CDD, will be presenting a talk, “Ensuring Chemical Structure, Biological Data and Computational Model Quality” Dr. Barry Bunin, CEO of CDD, will be [...]
CDD 2015 Holiday Haiku December 15, 2015 - The Agnostic Drug Hunter...
Dark Chemical Matter in Drug Discovery: When Compounds Simply Won’t Work December 7, 2015 - Over the years, thousands and thousands of compounds have been tested over an ever-increasing number of targets and assay conditions. And while it is expected to find most compounds in screening exercises to be inactive, nobody previously had investigated if there were any compounds that would be inactive against any target/assay used to date.
Well, Novartis addressed this question in a recent publication in Nature Chemical Biology. In this study, the authors looked into the Novartis screening deck and the NIH’s Molecular Libraries collection, identified those compounds that were inactive in at least 100 assays (Novartis: 234 assays; NIH: 429 assays), and coined a new label for these compounds: Dark Chemical Matter (DCM).
This study brings to light that there are compounds that for unknown reasons are simply inactive in many biological assays. Clearly, robust database software with assay analytical and data visualization capabilities like those found in CDD Vault and CDD Vision help rapidly ID activity cliffs. Yet, with any tools, perhaps the darkness associated to compounds can be better understood over time as a function of the type of assay, target pursued, and biological assay conditions.
Who is to say that one of these dark compounds wouldn’t be active in an assay in some other research group or company...
CDD Vault Update: Usability enhancements December 4, 2015 - This release introduced several handy enhancements to CDD Vault: streamlined Explore Data sidebar supporting projects between vaults, color-coded plate summary statistics on the Run Summary tab, streamlined project membership interface, and streamlined sharing and removal of resources in projects. We have also added keyword searching for solvent data.
Lights, Camera, Action…CDD Vault Hits the Red Carpet! December 2, 2015 - In this fast-paced action-packed video, the researchers at the Martin Research Group take us on an epic quest for knowledge. You’ll share their struggles, feel their pains and celebrate their victories as CDD Vault helps Michael and his lab mates locate the available chemical derivatives for a proposed Alzheimer’s treatment. This nail-biting journey will take [...]
Drug Discovery Thought Leadership Webinar: Review, Summary, Follow-up and Recordings November 17, 2015 - On November 4th, 2015, CDD hosted a live webinar where thought leaders discussed the challenges of modern drug discovery. For those who could not attend, we invite you to review this summary and follow these links to the webinar recordings. Panelists’ discussion: Retrospective analysis can be useful for limited domains, yet lessons are often not [...]
Videos on Changes in Drug Discovery Thought Leadership Webinar November 11, 2015 - Our recent CDD Webinar by industry thought leaders with the scientific community discussed why innovation and synergy are critical to drug discovery project team success is now live online.
CDD was joined in the discussion by:
* Daniel Erlanson (President), Carmot Therapeutics
* Mark Gurney (CEO), Tetra Discovery Partners
* Henry Johnson (Principal Scientist), Kezar Life Sciences
* Shirley Louise-May (CDD Advocate), ex-Pfizer
* Nicholas Skelton (Principal Scientist), Genentech
Our previous CDD Webinar case study with viDA Therapeutic’s Dr. Dale Cameron on how innovation and synergy was implemented...
CDD Presents at the International Chemical Congress of Pacific Basin Societies in Honolulu, Hawaii, in December 2015 November 5, 2015 - CDD presents talk and poster at the 2015 International Chemical Congress of Pacific Basin Societies in December Aloha! CDD will be attending and presenting at the 2015 International Chemical Congress of Pacific Basin Societies. This conference is scheduled for December 15-20, 2015, in Honolulu, Hawaii. The PacifiChem Congress will be held at the Hawaii Convention [...]
Ninth Chapel Hill Pharmaceutical Sciences Conference – Frontiers in chemical biology: transforming drug discovery October 16, 2015 - CDD co-sponsored conference meeting summary
From the desk of Sean Ekins, CSO
Yesterday I attended the Ninth Chapel Hill Pharmaceutical Sciences Conference which was co-sponsored by CDD. I was not alone as there was a large audience of graduate and post graduate students and professors, easily in excess of 250.
We were treated to 8 exceptional talks from luminaries in the field of chemical biology as follows.
Kevan Shokat (UCSF) – Nontraditional approaches to drugging traditional targets: kinases and GTPases
Tom Muir (Princeton University) – Painting Chromatin with synthetic protein chemistry
Donald McDonnell (Duke University) – ERRα regulated lactate metabolism contributes to resistance to targeted therapies in breast cancer
Bryan Roth (UNC at Chapel Hill) – Exploring the subterranean biology of known drugs...
CDD Vision Update: Histograms October 12, 2015 - This update brings histograms to CDD Vision, and more flexibility in setting scatter plot scale ranges.
On Demand Video from the Wrangling all your Diverse Assay Data Webinar October 8, 2015 - CDD’s recent live webinar event, Wrangling all Diverse Assay Data, was a great success. To summarize, Dr. Dale Cameron discussed how viDA Therapeutics implemented CDD Vault, saving time and money by leaving behind the “large amount of labor it took” to maintain multiple tools. This webinar demonstrated firsthand how a hosted, secure collaborative system makes [...]
From the desk of CDD Vault’s early customer Professor James McKerrow October 6, 2015 - The 2015 Nobel Prize in Physiology or Medicine was awarded to three scientists who pioneered the search for drugs to treat neglected tropical diseases (NTDs). Their efforts parallel and validate the commitment of CDD to provide computational searches and database management in support of research targeting these diseases of global health importance.
William C Campbell and Satoshi Omura shared one half of the 2015 Nobel Prize for their discovery and development of avermectin and its analog ivermectin. Ivermectin has played a major role in stopping the transmission of River Blindness in the New World and lymphatic filariasis throughout the tropical world. Youyou Tu was awarded the other half of the Nobel Prize for her discovery of artemisinin, the current drug of choice for malaria. The recognition of the work of these scientists by the Nobel Committee is validation to the efforts of CDD and their global partners in addressing the need for drugs, vaccines, and diagnostics to control, and perhaps someday eliminate, neglected tropical diseases. In fact CDD was launched in 2004 as a spinout of Eli Lilly with the Director of the Sandler Center for Basic Research in Parasitic Diseases at the University of California San Francisco as a key early customer foreshadowing our growth over the last decade for neglected and commercial drug discovery...
Nobel Prize for neglected parasitic diseases: Could it spur more treatments? October 5, 2015 - CDD is committed to working on neglected diseases for no other reason than because it is the ethical and right thing to do. Every year millions of our brothers and sisters around the world perish because they happen to live in a region where parasites, bacteria or viruses coexist for which treatments are not accessible, too expensive, too toxic, or worse still, they just have not been discovered. It seems almost too medieval to think that people are dying in the millions because of the equivalent of modern day plagues brought on by microscopic entities that have surrounded us in some cases for millennia.
Today we celebrate 3 scientists who made a dent in some of these diseases. William Campbell and Satoshi Omura won for their work on discovering Avermectin which lead to treatments for River Blindness and Lymphatic Filariasis. Youyou Tu also won for her work on Artemisinin as a treatment for malaria...
CDD To Attend the 2nd Annual Oxford Global Drug Discovery USA Congress in October 2015 in Boston, MA September 30, 2015 - CDD will attend and exhibit at the Oxford Global Drug Discovery USA Congress on October 29th and 30th, 2015 at The Westin Boston Waterfront Hotel in Boston, MA. Come visit us in Booth 3. CDD will be exhibiting the latest developments in our hosted solution for bioassay data management, chemical registration, and Structure Activity Relationship [...]
For 3D Vision, Mine PDB Ligand Structures in CDD Vault (Part 2 of 2) September 28, 2015 - For 3D Vision, Mine PDB Ligand Structures in CDD Vault Guest blog from CDD Advocate: Dr. Dale Cameron Part 2 of 2 In a recent blog post, CDD announced the addition of the latest ligand structures from the Protein Data Bank (PDB) into the CDD Vault®. The expanded availability of this unique and useful data is indeed [...]
CDD Spotlight Interview with Ronnett Seldon, University of Cape Town, South Africa September 15, 2015 - Interviewed by Collaborative Drug Discovery, Inc.
When you joined H3-D were they already using CDD Vault?
Yes, CDD Vault is a central database so everybody has access to the data. I have been with the project for 18 months now, and I run a dose-response inhibition assay which generates a significant amount of data analysis. I had intended to use GraphPad prism or Stata for my analysis in which I have to define controls and use a 4 parameter logistic regression for the curve generation. For large data sets, this takes a lot of time. I am a clinical research microbiologist, so I have a fair amount of experience with large datasets.
While uploading data to CDD, I noticed in the help section of CDD Vault that the platform has a customized 4-parameter logistic regression that is used to process and analyze the data. This has changed, a whole lot and for the better, the amount of time I need to upload and process the data. CDD Vault is not just a database to which I bulk upload data, but I actually use it to analyze and process all my data...
You need a new database for your chemistry and biology data – but you wonder if the switch will be too much work? September 9, 2015 - From the desk of Dr. Sylvia Ernst, Head of Sales and Sales Operations:
"CDD Vault makes it easy and the CDD team will help ensure a smooth transition"
How, you ask? What should you do when you really need to modernize your biology and chemistry data management, and yet the change feels like a colossal task? Let’s shed some light on the concerns we’ve heard and maybe the update will be easier than you imagined.
Concern #1: We have so much legacy data which we continue to use. How can we get the existing data quickly into new, improved systems and processes?
Concern # 2...
Want 3D Vision? Protein Data Bank (PDB) Ligand Structures are now LIVE in CDD Vault® (Part 1 of 2) August 26, 2015 - PDB ligand structures are now LIVE in CDD Vault®
Guest blog from CDD Advocate: Dr. Dale Cameron
The very best medicinal chemists can think in 3D about the compounds they design (both in the absence and presence of a molecular target). They appreciate that 3D structures are dynamic, dependent on their environment and important for optimizing candidate properties.
Ligand-target co-crystallization data can augment traditional structure activity relationship analyses. Now you can collectively consider your proprietary data within CDD Vault® using the latest ligand structures from...
CDD Vault Webinar: Wrangling all your Diverse Assay Data August 20, 2015 - Online Webinar: Wed Sept 30th at 9am PT, noon ET, 4pm GMT
A collaborative webinar by Dr. Dale Cameron (viDA Therapeutics) with Dr. Barbara Holtz and Charlie Weatherall
Have you ever wondered about the cost vs benefits of a shared resource for your full project team? What are the benefits versus sharing excel files or traditional databases for screening biologists, medicinal chemists, and other key collaborators? How can it work?
Find out how viDA Therapeutics (and you) can save time and money relative to the "large amount of labor it took" to maintain multiple tools. How did a project team go from starting out using just flat files to mach-6 with CDD Vault. Why was it the right solution and the right time? Why did they buy? How did it work and even exceed expectations?
See first-hand how a hosted, secure collaborative system makes information available for...
CDD To Attend the Frontiers in Medicinal Chemistry Conference in September 2015 in Antwerp, Belgium August 20, 2015 - CDD will attend and exhibit at the Frontiers in Medicinal Chemistry Conference on September 14-16, 2015 at the University of Antwerp (City Campus) in Antwerp, Belgium. Come visit us at our booth. CDD will be exhibiting the latest developments in our hosted solution for bioassay data management, chemical registration, and Structure Activity Relationship (SAR) analyses. [...]
CDD Vault Update: Visualize Many Plots, Transcend your Vault August 14, 2015 - This release introduces more projects in CDD Vault, and more plots in CDD Vision. Projects between Vaults allows groups collaborating across several vaults to search and visualize their data side-by-side in a single view. CDD Vision is enhanced with multiple scatter-plots. 
New White Paper: Promoting Effective Project Teams for Drug Discovery August 6, 2015 - Meeting the Informatics Needs of All Team Members When only 1 in 10 drugs tested in humans gets to the market, and those take 10-12 years to go through the process, it’s amazing when any drug discovery and development team is successful! A new white paper is available which explores the mechanisms for meeting the [...]
CDD CEO Barry Bunin Featured in SLAS ELN Interview July 20, 2015 - Before The Cloud was a regular part of our lexicon, entrepreneurs such as Barry Bunin pioneered secure, collaborative data hosting for scientists. “We have all the ideas for a Nobel Prize here in this lab. The problem is that the ideas are in separate brains instead of one. If we could gather everything into one [...]
CDD Hosts Workshop, Presents Papers and Posters at the 250th ACS National Meeting & Exposition in August 2015 July 16, 2015 - CDD hosts CDD Vision Workshop while Dr. Sean Ekins (CDD’s Chief Scientific Officer) presents papers and posters at the 250th ACS National Meeting & Exposition in August 2015 Dr. Ekins’ presentations will be part of the technical program at the 250th ACS National Meeting that will be held in Boston, MA. YOU are Invited to [...]
Rapid prototyping From TB Mobile to CDD Models July 8, 2015 - Rapid prototyping From TB Mobile to CDD Models From the desk of CDD CSO Sean Ekins, M.Sc., Ph.D., D.Sc. If I have seen further it is by standing on ye sholders of Giants – Isaac Newton As someone working in drug discovery you cannot escape what appears to be the vast number of papers (and [...]
Some Clouds Are Lined With Silver, Some Are Lined With Gold July 1, 2015 - As a research scientist in the health field, concerned with hastening the pace of therapeutic advances, my pulse quickens at the thought of clouds laden with research data, coalescing into a storm of Eureka moments. I imagine new collaborations and alliances producing a rain of ideas and hypotheses to quench the drought of therapies for the many ills that plague our bodies.
While Google and Apple wrestle over who will siphon the most data into their private storehouses, other companies and organizations have established and promoted the Cloud as a conduit for collective gains, offering the vision and potential for a Cloud lined with gold....
Machine Learning Models and Pathway Genome Data Base for Trypanosoma cruzi Drug Discovery published in PLOS Neglected Tropical Diseases June 26, 2015 - We are pleased to announce that the results of a phase I STTR collaborative study on Chagas Disease with groups at SRI International, UCSD, and UCSF have just been published in PLOS Neglected Tropical Diseases.
Chagas disease is a neglected tropical disease caused by the eukaryotic parasite Trypanosoma cruzi. We used a combination of cheminformatics, bioinformatics, in vitro and in vivo testing to identify molecules active at eliminating the parasites from infected cells. We found that the European Medicines Agency approved antimalarial drug pyronaridine possessed 85.2% efficacy (reduction in parasite burden compared to untreated control group after 4 days treatment) in the acute Chagas mouse model and may represent a repurposing opportunity.
This study also utilized the public T. cruzi datasets present in the CDD Vault. “This project demonstrates what can be achieved by combining complimentary approaches...
CDD Vision Update: Launching Vision now May 2, 2015 - We’re thrilled to announce the inaugural release of CDD Vision. Fully integrated with CDD Vault, CDD Vision provides powerful and intuitive visual analysis and plotting features. Whether you are a biologist looking for selective compounds, or a medicinal chemist looking to optimize chemical properties of active compounds, CDD Vision provides the tools to analyze and [...]
CDD Presents Papers and Posters at Cambridge Healthtech Institute’s Twelfth Annual Mastering Medicinal Chemistry in June 2015 April 29, 2015 - Dr. Barry Bunin (CDD's President and CEO) will present papers and defend posters at the 2015 Mastering Medicinal Chemistry in June 2015 at the Westin Waterfront in Boston, MA
Come visit us in Booth 18
CDD will be exhibiting the latest developments in our hosted solution for bioassay data management, chemical registration, and Structure Activity Relationship (SAR) analyses. Please visit us at Booth 18 in the Exhibit Hall between June 10-11, 2015, to witness the power and flexibility of CDD Vault...
On Demand Video from the pIC50 Scientific Webinar April 15, 2015 - CDD’s recent live webinar event about the merits of pIC50 was a great success. To summarize, Dr. Marc Navre endeavored to convince the audience to think logarithmically, and why the use of pIC50 values to share the results of in vitro assays with colleagues is easier, smarter and cleaner than using “old-fashioned” IC50 values. Live examples of using CDD Vault and CDD Vision to enable these calculations were also presented.
If you missed it, or would like to share with your colleagues, you can download the slides or check out the complete presentation...
Collaborative Drug Discovery Books – Part 2 March 31, 2015 - When we are not writing code, planning strategy, or increasing customer delight here at CDD, we learn from a variety of books covering topics. Here in part two we look deeper within the brain to see what drives us all, how to drive better, and how we can collaboratively synergize given the nature of group dynamics. We'd like to share these five additional books you may find interesting...
Collaborative Drug Discovery Books March 16, 2015 - When we are not writing code, planning strategy, or increasing customer delight here at CDD, we seek enrichment from a variety of books covering topics from drug discovery to discovery at large. Discovery as the quest for novelty, is one the great motivators for all researchers. And insights come from some unlikely sources, like from the "theater" of the emergency room or the lessons of persistence leading to the first antibiotic.
We'd like to share with some books you may find of interest:
The Demon in the Microscope...
CDD To Attend the 2015 Bio-IT World Conference & Expo in April 2015 March 9, 2015 - CDD will attend and exhibit at the 2015 Bio-IT World Conference & Expo in April 2015 at the Seaport World Trade Center in Boston, MA
Come visit us in Booth 152
CDD will be exhibiting the latest developments in our hosted solution for bioassay data management, chemical registration, and Structure Activity Relationship (SAR) analyses. Please visit us at Booth 152 in the Exhibit Hall between April 21st and April 23rd, 2015...
Databases and collaboration require standards for human stem cell research February 20, 2015 - Last year CDD has published a review about databases and collaboration in the area of human stem cell research. The article is now published in Drug Discovery Today * and you can get a free copy for the next month or so. The goal of the article was to examine the current public data space in stem cell research, and to find the gaps. We also provide an example of how the CDD Vault can be used to solve the main problems of secure data sharing...
CDD Vision Update: More Calculations with Protocol Conditions February 14, 2015 - This release adds new features to protocol conditions and dose-response calculations. In summary, you can now specify multiple condition values in your custom formulas, your search results will now show a separate column for each protocol condition, and you have more flexibility when defining dose-response curve validation.
CDD chairs sessions, presents papers and defends posters at 22nd International Molecular Medicine Tri-Conference in February 2015 February 7, 2015 - Dr. Barry Bunin (CDD's President and CEO) will present papers, defend posters and chair sessions at the 22nd International Molecular Medicine Tri-Conference in February 2015 at the Moscone North Convention Center in San Francisco, CA
Come visit CDD in Booth 3
CDD will be exhibiting the latest developments in our hosted solution for bioassay data management, chemical registration, and Structure Activity Relationship (SAR) analyses. Please visit us at Booth 3 in the Exhibit Hall between February 16th and 18th, 2015, to witness the power and flexibility of CDD Vault.
Accelerated Drug Discovery Perspectives Given the Ebola Virus Outbreak February 3, 2015 - Like many around the world, we have been watching the devastating effects of the Ebola Virus in West Africa. We have been impressed by the important contributions of the health organizations and medical workers that have served patients at great personal risk to themselves and brought the disease under some degree of control. Especially during a crisis, seamless effective collaborations are critical. Collaboration can catalyze the communication of current knowledge and coordinate future action – whether for drug repurposing or de novo drug discovery. We wondered, how can those of us in drug discovery contribute in some way? We have found considerable interesting published results regarding molecules showing some activity against the Ebola Virus, including a number of FDA-approved drugs and made them available as a public data set in CDD Vault for the scientific community. 
CDD Vault for medicinal chemistry decision support in large collaborations January 21, 2015 - Last week I attended the More Medicines for Tuberculosis (MM4TB) consortium meeting in Bilbao Spain. The MM4TB consortium consists of over twenty partners from thirteen countries in Europe, America, Asia and Africa. This event happens twice a year and represents an opportunity to bring the various groups together to discuss scientific progress. The meetings are also a chance to socialize with colleagues and share TB experiences and insights over two full days of work and leisurely lunches and dinners.
CDD to Present at SLAS Meeting in February January 12, 2015 - CDD will be presenting two scientific talks at the upcoming Society for Laboratory Automation and Screening (SLAS) Conference in Washington, DC, between February 7th and 11th, 2015. Dr. Barry Bunin, CEO of CDD, will be chairing one of the Informatics sessions and presenting a talk entitled “10 Years Securely Hosting Collaborative Drug Discovery CDD Vault [...]
Beware Researchers! Challenges Navigating Commercial and Public Databases December 16, 2014 - From the desk of CDD CSO Sean Ekins, M.Sc., Ph.D., D.Sc. Each of the phases of a drug discovery project is directly impacted by the quality and availability of relevant data. There is no question that well-curated chemical structures and linked bioactivity data enable drug discovery projects. This is true whether managing a single organization, sharing [...]
CDD Vision Update: Calculations with Protocol Conditions December 13, 2014 - The full power of recently introduced protocol conditions is realized with this release, incorporating conditions into CDD Vision calculations. This means your data entry and management is simplified with fewer protocols, and data processing and analysis is flexible and powerful using conditions.
It’s all about the data, ‘bout the data, no trouble – CDD Holiday Poem December 5, 2014 - The holiday season is a time of retrospection and merriment. At CDD, we have a tradition of a sharing a holiday poem (See 2013, 2012, 2011, etc.). This year, we’ve been a bit more playful and have written this year’s poem to the catchy tune of Meghan Trainor’s “All About That Bass” which has been [...]
CDD Vault Update: Averaging numbers with modifiers November 26, 2014 - In this update, we have changed the way numbers with numeric modifiers, such as IC50 values, are averaged. Previously imported data were automatically recalculated following the new rules, which are better suited to drug discovery applications.
Whoa! Our Customers Are Just The Best! November 20, 2014 - These lighthearted videos from the Martin Research Group at the University of Texas just made our day! We at CDD laughed until we cried with appreciation of all the creative work those guys and gals put into producing these awesome videos. We appreciate the subtle humor and are grateful for their creative way of sharing the “happy CDD Vault user” experience.
Let us know which scene is your favorite...
Machine Learning from an Expert’s Evaluation of Compounds November 14, 2014 - CDD has recently developed, as part of CDD Vision, the ability to build machine learning models. These can be used to make predictions for properties of molecules that may not have been tested. Once a scientist chooses a “good” set of compounds, perhaps with a desired bioactivity, and a “bad” set, the inactives, with a single [...]
CDD Joins Ryoka at the 32nd Medicinal Chemistry Symposium in Kobe, Japan, on November 26-28, 2014 November 13, 2014 - CDD joins our Japanese distributor, Ryoka Systems, at the 32nd Medicinal Chemistry Symposium event in Kobe, Japan, on November 26-28, 2014 CDD, along with Ryoka Systems, will be attending and presenting at the 32nd Medicinal Chemistry Symposium (MCS2014), which will be held at the Kobe International Conference Center in Kobe, Japan, between November 26th and [...]
CDD’s CSO is scheduled to speak and present a poster at the In Silico Drug Discovery Conference in December 2014 November 11, 2014 - Dr. Sean Ekins (CDD's Chief Scientific Officer) is scheduled to speak and present a poster at the In Silico Drug Discovery Conference in December 2014
The In Silico Drug Discovery Conference will be held at the Hamner Conference Center in Durham, NC, on December 3rd and 4th, 2014. Dr. Sean Ekins, CSO at CDD, will be presenting a talk and a poster at the In Silico Drug Discovery Conference. The conference is being hosted by the North Carolina Biotechnology Center in the Hamner Conference Center, and is slated to include expert speakers, panelists, researchers, and product vendors.
CDD Launches CDD Advocate Program November 4, 2014 - Announcing CDD Advocate!!
In the spirit of collaboration, CDD is happy to announce the launch of the CDD Advocate program. This program is a network of professionals in the drug discovery research space dedicated to raising the awareness of CDD's very cool and unique technology, CDD Vault. At CDD, we've always understood the power of collaboration. As a progressive web company, we encourage collaborative ventures and are committed to our philosophy that working together is a crucial aspect to success in today's research environment.
Members of our CDD Advocate program will be...
CDD Announces Partnership With Ryoka Systems November 3, 2014 - Ryoka Systems becomes CDD Reseller in Japan Collaborative Drug Discovery (CDD) is excited to announce the appointment of Ryoka Systems as the Japanese distributor for CDD Vault. The new partnership makes this flagship platform broadly available with local support and customized training for researchers in Japan. CDD Vault is widely used for Structure-Activity (SAR) analysis, [...]
CDD Vault Update: Maximum Measured Activity November 3, 2014 - Concentration response calculations- minimum and maximum measured activity are now reported.
API addition- download readout rows by run ID instead of run date. CDD Vision gets an update: you can build a predictive model from a molecule collection. And the release notes move to the CDD blog.
CDD to Attend the 3rd Annual Conference of the International Chemical Biology Society (ICBS) in San Francisco in November 2014 November 1, 2014 - CDD will be attending the 3rd Annual Conference of the International Chemical Biology Society (ICBS) in San Francisco between between November 17th and 19th, 2014. Personal demonstrations are available at Booth TT-12 during the ICBS Conference! Visit us to witness first-hand the power and flexibility of CDD Vault, which combines a bioassay database and chemical [...]
In Case You Missed It, Check Out The Video From CDD’s Recent Scientific Webinar October 29, 2014 - CDD’s recent live webinar event was a great success. To summarize, first, Dr. Chris Lipinski, reknowned medicinal chemist and CDD Scientific Advisory Board member, described the importance of considering enthalpy and entropy when optimizing for ligand affinity, and how this might differ between drug discovery techniques. Using the custom calculations available in CDD Vision, we defined [...]
CDD Spotlight Interview with Thale Jarvis, Crestone Inc. October 23, 2014 - "People sometimes refer to it as drug hunting. It starts with early discovery, finding interesting compound libraries and screening for hits, followed by a lot of intensive medicinal chemistry, microbiological and biochemical characterization and preclinical testing. Once you have an IND candidate, the focus expands to include process chemistry and toxicology testing. And that’s before you even consider human clinical trials. It’s a long process, but terrifically engaging. You have to balance optimism with realism. It takes great teamwork; to succeed, your team has to be smart, tenacious and lucky in about equal measures."
Get Ready for CDD’s First Live Webinar Event! October 14, 2014 - In preparation for our webinar next week, we at CDD have been busy investigating trends across CDD Public datasets. With data on more than two million compounds and unlimited capability for generating custom calculations, there has been no shortage of intriguing findings. For example, when experienced medicinal chemist Chris Lipinski suggested that there may be [...]
CDD Vault Update: Improved Structure Editor October 11, 2014 - The Javascript-based structure editor we introduced earlier this year is great, but it was missing a few key features, such as support for direct copy and paste of structures. We are happy to report that this update should address the most common requests.
CDD Vault Donation for Ebola Researchers October 9, 2014 - In Western Africa, Ebola has already killed more than two thousand people, and the Center for Disease Control (CDC) has estimated up to 1.4 million people could contract the deadly virus in the coming months in a worst-case scenario. Despite the growing threat, there is still no therapy that can be distributed at a large-scale. [...]
A novel collaborative, fast-paced workflow: From a discussion on Twitter to a micropublication on Ebola October 3, 2014 - From the desk of CDD CSO Sean Ekins, M.Sc., Ph.D., D.Sc. We are all aware of the nightmare going on in Africa, and now elsewhere, regarding the spread of the Ebola virus. Although it is important to point out so far it has killed a small fraction of the hundreds of thousands that have likely [...]
A Conversation on Drug Discovery Biases September 18, 2014 - From the desk of Chris Lipinski, PhD I’ve been thinking a lot lately about how to optimize for ligand affinity. Of course, this is a central theme of all drug discovery projects. At its core is the question of how physical and chemical relationships guide the interplay between the ligand, the protein target, and the [...]
Announcing CDD’s First Live Webinar Event – Are Your Compounds Biased by Your Discovery Techniques? September 8, 2014 - Entropic and Enthalpic Propensities Inherent in SBDD and HTS. Dr. Christopher Lipinski Dr. Matthew Soellner Dr. Barry Bunin Online Webinar: Wed, Oct 22 from 2-3pm ET Christopher Lipinski’s decades of experience practicing medicinal chemistry for Pfizer and post-Pfizer have led him to believe that there are inherent biases in the molecules developed via different drug discovery [...]
CDD Innovation: A New Tool for Annotating Bioassays September 2, 2014 - CDD’s informatics research wing has been busy this summer. In a collaboration with the Bioassay Ontology Project at the University of Miami and funded by a NIH SBIR Phase I grant, CDD has prototyped a new tool for annotating bioassay data. Our method is fully described in this paper, just published in PeerJ: Fast and accurate semantic [...]
Collaboration in the Twitter Age August 28, 2014 - From the desk of CDD CSO Sean Ekins, M.Sc., Ph.D., D.Sc.
Scientific conferences can be huge ungainly affairs with tens of thousands of attendees spread over many concurrent sessions and possibly locations. These meetings are great for networking but it is likely any single attendee will only be exposed to the smallest fraction of the science being presented. How could anyone imagine capturing all the data or even a fraction of it presented orally let alone the content of the posters? Being unaware of the science may not be optimal in finding potential collaborators either. Good examples for chemists include...
CDD Vault Update: Image Sizes and Solvents of Crystallization August 20, 2014 - Adjustable image size in the search results table “Small” molecules come in a variety of sizes, and you can now adjust the structure images to suit your molecules and eyesight. Dose-response plots and images from uploaded files also scale to the same small, medium, or large previews in the search results table. The size is [...]
Collaboration Paves the Road for Ebola Treatment August 19, 2014 - In the throws of the largest Ebola outbreak ever, with more than 2000 confirmed cases in West Africa, there was a glimmer of hope when the little known biotechnology company Mapp Biopharmaceuticals gave their potentially life-saving drug, ZMapp, to two infected patients. ZMapp has very encouraging results in non-human primate studies, but has not been tested [...]
Making the NIH Chemical Probes (over half a billion dollars of NIH investment) accessible in CDD Public August 15, 2014 - The Molecular Libraries Program (MLP) has been a tremendous resource for academic labs to pursue the development of chemical probes in a wide range of biological processes. The National Institutes of Health (NIH) has funded extensive HTS efforts, by conservative estimates over half a billion dollars has gone into the program, and we wanted to [...]
CDD Spotlight Interview with Dale Cameron, viDA Therapeutics Inc. July 28, 2014 - "It was the first time in my career that I can remember, where creativity and outside the box thinking allowed for mixing and matching a lot of different and unrelated tools, to do something they weren’t originally intended, to generate a result that had immediate and positive effect on our research programs. Completely unpublishable work, I must admit, but...our own crystal structures would eventually come sometime later in the program, and when compared to our hand-made model of a model, we were very close, to the point where the crystal structure simply validated our model, which for a computational chemist, was intensely satisfying."
CDD Vault Highlighted in Scientific Computing Article July 24, 2014 - In the June 2014 issue of Scientific Computing, industry expert Michael Elliott heralds the emergence of robust cloud technologies to support research virtualization. “Collaborative Drug Discovery is the most mature of the group,” he points out, and we are flattered that he has noticed our pioneering position. He goes on to point out that new [...]
CDD Vault Update: Search Results and Z-Score July 19, 2014 - Full width search result table The search results table now uses the entire width of your screen, maximizing the data you can see without needing to scroll. Structure search limit The maximum number of structures matched by a similarity or substructure search has been increased to 100,000. A clear message is now shown when this [...]
Why using pIC50 instead of IC50 will change your life July 14, 2014 - A significant number of CDD Vault subscribers use IC50 values to store and analyze their dose response data from in-vitro assays. Now that the automated calculations extension of CDD Vision supports the calculation of pCI50 values, I’d like to convince users of IC50 to consider using pIC50 instead, and why it will make your life easier (in the long run), and just make you a finer human being.
Drug Discovery in the Age of the Customizable Genome: Implications of the CRISPR Revolution July 8, 2014 - The CRISPR/Cas9 system allows for unprecedented ease and access to editing the genome, offering drug discovery researchers creative and precise control when designing and developing screening assays. Application of CRISPR/Cas9 has spurred collaborations, led to key advances in diverse fields from neglected and rare diseases to cancer and gene therapy, and has the potential to shift the landscape of drug discovery.
CDD (including CDD’s CEO & CSO) is scheduled to chair sessions, present papers and defend posters at the 248th ACS National Meeting & Exposition in August 2014 June 30, 2014 - Dr. Barry Bunin (CDD’s President and CEO), Sean Ekins (CDD’s Chief Scientific Officer) and Adam Kallel have papers, posters, and session chairs at the 248th ACS National Meeting & Exposition in August 2014 These presentations will be part of the technical program at the 248th ACS National Meeting that will be held in San Francisco, [...]
CDD Vault Update: Calculations Using Multiple Protocols June 28, 2014 - The flagship feature of this release is the ability to perform calculations using results from multiple assays. This allows you to calculate the selectivity index and similar metrics. Calculations between protocols – part of CDD Vision The readout definitions you use in calculations can now come from multiple protocols. Like all calculations in CDD Vision, [...]
CDD’s Public Database is a Valuable Resource June 24, 2014 - CDD Public offers CDD Vault users access to more than 100 well-curated datasets that can be easily mined and analyzed in conjunction with your own private data. Compounds stored in CDD Public can be easily searched and filtered using the CDD Vault‘s easy-to-use, chemically intelligent interface. In addition, CDD has recently developed the ability to [...]
CDD to Attend Enabling Future Pharma Conference in July 2014 June 12, 2014 - CDD will be attending the Enabling Future Pharma: Strategic Initiatives in Collaborative Innovation in Drug Discovery, Heralding the Mutually Inclusive Role of NIH, Academia, Pharma and Patient-Based Organizations Conference in Chicago between July 9th and 12th, 2014.
CDD’s CEO, Dr. Barry Bunin, is scheduled to present a talk in the "Cutting Edge Research-Tools, Technologies for Chemical Biology" track at 5:00 pm on Friday, July 11.
Dr. Bunin's presentation is titled “The Collaborative Drug Discovery Paradigm: Modern Drug Research Informatics Applied to CNS, Infectious, Neglected, Rare and Commercial Disease Applications”....
WIIFY Part 3 – Modern Drug Discovery Tools for Large Collaborative Consortia June 11, 2014 - A three part series exploring the unique challenges of Consortia scientists
Part 3 – What’s in it for you, the person who actually has to do the work
You are the one actually doing the work, the hard work that others eschew. Parts of science can feel like working in quicksand, with handcuffs on. There are multiple problems, and as soon as you fix a problem, new ones emerge. You must do reproducible science - the hallmark of good science. On top of all the experimental challenges, you have this mountain of data to deal with. Big data typically means big headaches. And whose lap does all this data fall into – why yours, of course. As if you are not busy enough? Isn’t it enough to just run all these experiments? Who has time to look at thousands or even millions of data points? Even worse than the numbers are the formats, the raw data from the plate readers or other instruments is different than the format needed to make heads or tails of the data relative to the controls you painstakingly included in the appropriate columns. When something unexpected happens (and when doesn’t that happen) like an instrument hiccup, or running out of a key reagent midway through a run, then the data must be looked at within the context of whatever the unexpected anomaly happens to be this time. Yes big data = big headaches. Well fret no more, you have a partner by your side each step of the way with CDD.
CDD has felt your pain and is your ally in the fight for your right to generate understandable, reproducible, and manageable data. Wasn’t that in the constitution somewhere?
CDD Vault Update: Calculations and Models May 10, 2014 - We introduce CDD Vision, a new analysis and visualization product, predictive model building within CDD Vault, and a half-dozen smaller enhancements. We are excited to see what you can achieve with the tools in this release. Calculations within a protocol – part of CDD Vision This is the introductory release of CDD Vision, an optional [...]
Open source ECFP/FCFP circular fingerprints in CDK May 10, 2014 - CDD Vault now allows you to build predictive models. Because we believe in collaboration and reproducible results, we are releasing the core algorithms that underly this feature as open source software. The chemical fingerprints are detailed below, and we have also released our modified Bayesian model. Send an email to info@collaborativedrug.com if you’d like to try using [...]
CDD Spotlight Interview with Enrique Michelotti, NIMH/NIH May 7, 2014 - "I think the biggest impact was people in academia that were not used to databases and with the training and the use, they came to realize how powerful it is to have a permanent central repository, where you can access the data very fast and correlate the most salient patterns. I think that is the most important impact by providing this new capability that was even useful for people that were just not used to databases. It really speaks to the ease of use and overall design of CDD Vault."
CDD Spotlight Interview with Paul Humphries, Reset Therapeutics April 17, 2014 - "As a company we all have to have a phenotypic drug discovery mindset, which means that we have to be prepared for any target (or working on an unknown target) that acts through any compartment (liver, CNS, etc) that modulates physiological endpoints for any disease. I’m no longer a target-based medicinal chemist working on metabolic diseases, I’m a phenotypic drug discovery scientist working on circadian modulators that are disease agnostic. It’s an exciting, challenging and hugely rewarding part of my career and I am relishing working with the Reset team to create a new path for drug discovery in this novel scientific area."
Part 2: CDD’s Tenth Anniversary Meeting Highlights April 14, 2014 - On Friday April 4th, CDD celebrated its tenth anniversary by hosting a community meeting at UCSF. We have written about the meeting before, but there is so much more to share that wasn’t covered. For starters, new CDD Vault tools were presented at the meeting, including calculations for the new CDD Vision module and QSAR models. [...]
Part 1: CDD’s Tenth Anniversary Meeting Highlights April 9, 2014 - On Friday April 4th, CDD celebrated its tenth anniversary by hosting a community meeting at UCSF. From all of us at CDD, we want to give a great big “Thank you!” to everyone who participated. We appreciate all those who prioritized their time out to fly/drive/walk to the conference, to present, to sponsor the event, to participate in panels, to listen attentively, and to ask questions. WOW! 
CDD to attend Drug Discovery Chemistry Conference in San Diego in April 2014 April 7, 2014 - CDD will be attending the Drug Discovery Chemistry Conference in San Diego between April 23rd & 25th, 2014. CDD’s Scientific Relations Consultant, Dr. Adam Kallel, is scheduled to present a poster at the Drug Discovery Chemistry Conference in San Diego between April 23rd & 25th. Dr. Kallel’s poster is titled “Leveraging CDD Vault®’s Kinome Data [...]
Reflections on World TB Day March 24, 2014 - My maternal grandfather died of tuberculosis. He contracted it while serving in the First World War. He returned from France to live a life of diminished quality, shortened by an early death. I can also remember, when I was a small child, in the 1970’s going for rides through Los Angeles’ Elysian Park area and passing what was then the Barlow Sanatorium. I asked my dad what a sanatorium was and was introduced at a young age to, what was still then, the isolating treatment of tuberculosis. The Barlow Sanatorium is now the Barlow Respiratory Hospital. Los Angeles, fortunately, no longer has the need for a facility dedicated to the treatment of TB.
CDD’s 10th Anniversary Community Meeting Agenda Now Online March 20, 2014 - If you haven’t already heard, we are celebrating our “10 Years of Collaborative Drug Discovery” by hosting a CDD user and community meeting at the UCSF Mission Bay conference center in San Francisco on Friday, April 4th. We have assembled an exciting day of presentations, panels, and discussion groups you can now see online (Agenda). [...]
CDD to attend Mastering Medicinal Chemistry Conference in May 2014 March 14, 2014 - CDD will be attending the 11th Annual Mastering Medicinal Chemistry Conference in Boston on May 21st and 22nd, 2014. CDD’s CEO, Dr. Barry Bunin, is scheduled to present a talk in the “Case Studies Session: Part III” track at 11:05 am on Thursday, May 22. Dr. Bunin’s presentation is titled “Modern Drug Research Informatics Applications [...]
CDD Vault Update: Averages and Normalization March 14, 2014 - Readout definitions: more flexible averaging You can now choose a different level of aggregation for each average readout, whereas previously the aggregation level was uniformly set for all readout definitions in the vault. The available aggregation levels are as follows: Batch/Run is good for replicate data in a single experiment (run). Replicated data from the [...]
Remembering Dr. Zaffaroni March 8, 2014 - When I first became an entrepreneur the one person whom I especially wanted to work with was Dr. Alejandro Zaffaroni. I was blessed to have some unique experiences working with him that I thought would be worth sharing. As many of you know, Dr. Zaffaroni was involved in fundamental biotech innovations ranging from the birth control pill to the patch to the Affymetrix gene chip. Generally he'd be involved on the technical, business, and people sides. On March 1 2014, at age 91, Dr. Zaffaroni passed away. His inventions of course impact many lives, yet how he worked directly with people was equally compelling. Mario Rosati once mentioned to me that Dr. Zaffaroni was the best he had seen in a board room. I thought I would share a few personal stories from my own interactions with him that have stuck with me over the years.
KeytoLead AB and CDD, Inc. would like to invite you to their joint seminar March 6, 2014 - KeytoLead AB and CDD, Inc. would like to invite you to their joint seminar: Medicinal Chemistry and Data Management in Modern Drug Discovery 27th March 2014, 14:00‐16:30 Apotekarsocietetens bibliotek, Wallingatan 26A, Stockholm Through clever medicinal chemistry, KeytoLead advances drug discovery targets into high‐quality starting points tailored for the pharmaceutical industries’ pipelines. KeytoLead manages entire lead [...]
WIIFY Part 2 – Modern Drug Discovery Tools for Large Collaborative Consortia March 5, 2014 - A three part series exploring the unique challenges of Consortia scientists Part 2 – What’s in it for you, the Lead Scientist funded by an external source You love science. That is why you became a scientist. You are good at it. You like being part of the scientific conversation mirrored in the literature and [...]
CDD Vault Update: Preventing Duplicates February 28, 2014 - This release makes it easier for you to avoid registering duplicate structures and includes a collection of other enhancements. Tautomeric structure detection When new structures are registered in the CDD Vault, they are compared to existing molecules. If equivalent structures are found by InChIKey, a suspicious “unintentional duplicates” event is reported. When this event is [...]
WIIFY Part 1 – Modern Drug Discovery Tools for Large Collaborative Consortia February 25, 2014 - A three part series exploring the unique challenges of Consortia scientists Part 1 – What’s in it for you, the person ultimately responsible for extracting value from a collaborative mixture of heterogeneous academic, CROs, and drug discovery brains. You have been successful in your career. And your reward is the enormous responsibility of advancing a [...]
CDD’s CEO & CSO to present papers and chair sessions at 247th ACS National Meeting & Exposition in March 2014 February 13, 2014 - Dr. Barry Bunin (CDD’s President and CEO) and Sean Ekins (CDD’s Chief Scientific Officer) will present papers and chair sessions at the 247th ACS National Meeting & Exposition in March 2014 These presentations will be part of the technical program at the 247th ACS National Meeting that will be held in Dallas, Texas. Podium [...]
WIIFY Part 3 – Modern Drug Discovery Tools for ex-Pharma Scientists February 11, 2014 - A four part series exploring the unique challenges of ex-pharma scientists Part 3 – What’s in it for you, the pure scientist? You were attracted to science because of the purity of the pursuit. You saw the opportunity to examine nature as it is, as objectively as possible. You saw a way to do some [...]
WIIFY Part 2 – Modern Drug Discovery Tools for ex-Pharma Scientists February 4, 2014 - A four part series exploring the unique challenges of ex-pharma scientists Part 2 – What’s in it for you, the manager of the group, the person on the hook if the project succeeds or fails? Whether you have a small group handling all experiments internally, or a distributed team spanning the globe, you need to [...]
WIIFY Part 1 – Modern Drug Discovery Tools for ex-Pharma Scientists January 28, 2014 - A four part series exploring the unique challenges of ex-pharma scientists Part 1 – What’s in it for ex-pharma scientists who need to make magic happen on a shoestring? You used to work in Big Pharma. So you know what it takes, what it really takes, to generate a rock-solid compound. You’ve seen integrated teams [...]
CDD to attend Molecular Medicine Tri-Conference in February 2014 January 27, 2014 - CDD will be attending the 21st International Molecular Medicine Tri-Conference in San Francisco between February 9th and 14th, 2014. CDD’s CEO Dr. Barry Bunin is scheduled to chair the “Pre-Competitive Collaboration & Supporting Public-Private Partnerships” track beginning at 2:15 pm on Tuesday, February 11, in the “Integrated R&D Informatics & Knowledge Management” channel. Dr. Bunin [...]
CDD Vault Update: Bigger and Better Chemistry January 24, 2014 - We’ve upgraded our chemistry software and replaced the structure editor. The new ChemAxon Marvin Javascript-based structure editor loads faster and won’t break every time there is a Java security update. Snazzy! New structure editor Marvin for JavaScript, the new structure editor, is used throughout the CDD Vault. It loads quickly, is independent of Java, and will [...]
CDD to attend SLAS meeting in January 2014 January 3, 2014 - CDD will be attending the 3rd annual Conference & Exhibition hosted by the Society for Laboratory Automation and Screening (SLAS) in San Diego between January 20th and 22nd, 2014. CDD’s CSO, Dr. Sean Ekins, will be presenting a talk and a poster at the 3rd Annual Conference & Exhibition hosted by the Society for Laboratory [...]
2013 CDD Holiday Poem – As People We Care December 1, 2013 - Commercial, neglected disease – Nature indifferent Mechanisms, molecules, methods persistent A molecule is a molecule, a sequence, a sequence A curve is a curve, an equation’s transcendent Money is indifferent, as it well should be But as people we care about malaria and TB And T. brucei, T. cruzi, don’t forget leishmaniasis Which rolls off [...]
A Call to Participate in a Data Sharing Initiative for Neglected Tropical Disease Drug Discovery November 26, 2013 - From the desks of Northeastern Professor Michael Pollastri and CDD CEO Barry Bunin:
Neglected tropical diseases (NTDs) affect over a billion poor people globally. Since there are relatively limited resources to discover new treatments, it is more critical that the those limited resources work optimally together. Efficient collaboration is the key to saving money, time, and to accelerating the drug discovery process.
Since we are already using the CDD Vault for our private collaborations, we are running an experiment with a separate CDD Vault involving selective (secure) sharing with a larger set of Neglected Tropical Disease Researchers. We have made an open call to other NTD labs from around the world to merge their drug discovery data with ours to identify areas of synergy and overlap. 
Help Us Build Innovative Products Customers Love November 22, 2013 - There’s something very special about working in an environment where your customers truly appreciate the quality and responsiveness of the products you dedicate your working life to build. If you would like to help develop the next generation of informatics systems for collaborative drug discovery research, consider a career with CDD. Dr. Kristina Bender from Stanford recently [...]
CDD Vault Update: Search page updates November 22, 2013 - This release brings a collection of handy enhancements to your searches and reports. “Not in” protocol search Have you ever wanted to find molecules that have NOT been tested in an assay so that you can schedule them for testing? With this release we add a “not in protocol” search that allows you to do [...]
CDD Vault Update: New import and search capabilities November 1, 2013 - Update structureless molecules en masse (For vaults that use CDD’s molecular registration system) If you work in a vault with a registration system, you previously had to manually update each structureless molecule when the structure became available. That’s fine for the one-off compound, but a drag for a whole compound library. Now you can bulk [...]
WIIFY Part 5 – Modern Drug Discovery Tools for Startup, Small Biotech, or Academics October 22, 2013 - What’s in it for you as a technician in a budget sensitive startup or academic laboratory, where you are running the experiments, generating the data, and perhaps even maintaining the instruments. Your lab is an intellectual (perhaps self-righteously so) place, but you are the one who actually does the final experiments that generate the screening [...]
CDD Vault Update: Batches can have files too October 11, 2013 - The last two releases brought you files-as-readouts. Now you can treat files as a special type of batch field. What does this mean? It means that you can associate images and other files directly with your structures! NMR spectra, MSDS sheets, crystal structures, requisition forms; you get the idea. Vault administrators will need to define [...]
CHARMMing Trio win Nobel Prize in Chemistry October 10, 2013 - Yesterday Martin Karplus, Michael Levitt and Arieh Warshel won the Nobel Prize in chemistry. Essentially their work has revolutionized computational chemistry and anyone that performs molecular simulations will know of their foundational work well. They basically developed CHARMM.
Much was written about their achievements, some of the press was just vague, claiming importance in many areas from solar cells to drug discovery, but anyone with knowledge of computational science could
Prof. Jonathan Baell of “PAINS” Filters Fame from Monash University October 7, 2013 - "People are just finding compounds with a bit of activity and really publishing screening hits as though they are genuine optimizable candidates. And these things can be subversive and they can look real, so these publications are kind of getting accepted and unfortunately there's a lot of noise out there, a lot of pollution, and this is one of the things we certainly strive to do here is not to publish something for the sake of publishing, but to publish it after making optimizations showing these are absolutely real."
CDD Vault Update: Do more with your files September 27, 2013 - Bulk file import Last week we debuted files-as-readouts: the ability to attach a file to any experimental result, and view a preview of the file’s contents throughout your CDD Vault. But what if you have 10,000 files you’d like to store? Here’s how: multiple files can now be attached during a single import by uploading [...]
Interview with Jill Wood September 27, 2013 - We think that out of the 4 types of Sanfilippo, type D is in the best position for an effective treatment. Type D is also a relatively mild form of the disease compared to Types A, B and C. It is hypothesized that with just a small increase in enzymatic activity, the disease could be drastically improved. A mouse model of the disease and a better understanding of the brain pathology of the disease, will assist us in developing a treatment. It is JJB’s aim to champion Type D research (alongside that of Type C), using our consortium of investigators to test treatments that we are already funding for type C and translate them and test them for type D. We recently learned that we were successful and had won the KO mouse development prize! The press release came out from Taconic who will kindly develop the mouse and donate it to us.
We actually submitted two proposals and we won part of what we had requested to help support our collaborations to find small molecule treatments for Type C. The judges awarded us the CDD Vault prize, so we are looking forward to putting that into action with our scientists and getting them to share their results securely!!
WIIFY Part 4- Modern Drug Discovery Tools for Startup, Small Biotech, or Academics September 17, 2013 - WIIFY – for the Collaborative Scientist: The CDD Vault technology facilitates real collaboration around data and people. The instant you or others see important trends for an interesting hit series, you can save a search with specific criteria to automatically detect future trends. You can ask better questions and you get better answers. As experiments [...]
CDD to attend ADDC meeting in October 2013 September 12, 2013 - CDD will be attending the annual Academic Drug Discovery Consortium conference in Nashville from October 9th through 11th, 2013. Come visit us at Booth 20 at the ADDC Exposition to witness the power and flexibility of CDD Vault. The Academic Drug Discovery Consortium was founded in November 2011. Its goal is to create a network [...]
CDD to present at the 7th annual Extremely Large Databases Conference in September 2013 September 4, 2013 - CDD’s Head of Scientific Informatics, Krishna Dole, will be presenting at the Extremely Large Databases Conference at Stanford University on September 10th, 2013. Krishna’s talk, titled “Scaling the CDD Vault Technology for a Global Community of Drug Discovery Researchers’ Private and Public Use Cases”, will be part of the Lightning Talks session starting at 3:00 [...]
CDD Vault Update: Dose-Response Extraordinaire August 30, 2013 - This release brings many sought-after enhancements for dose-response curve fitting, such as overriding IC50s and constraining fit parameters for individual curves. Plus much more; keep reading to find out! Amidst all of these features for biologists, we’ve added one new feature for chemists especially: preserving molecule orientation as drawn. For chemists Preserve molecule orientation and [...]
CDD at The Science and Tech Forum Sept 28th in Los Angeles August 20, 2013 - Join CDD’s CEO & President, Dr. Barry Bunin, at The Science and Tech Forum: Los Angeles as he discusses modern drug research informatics applications to CNS, infectious, neglected, rare, and commercial diseases. This forum looks to the future of scientific research by focusing on the tools of 21st Century communication and how they are changing [...]
Dr. Robert Volkmann, Vice President of Chemistry – Mnemosyne & SystaMedic August 15, 2013 - "What you've done is you've designed a product that works for people like me. It not only works great for me but also works great for our biologists and our CRO chemists in India. ... I just take it for granted that CDD Vault will work and it will work as planned. So I guess for me the test for the value of something is that you can use it without ever thinking about it."
WIIFY Part 3 – Modern Drug Discovery Tools for Startup, Small Biotech, or Academics August 8, 2013 - What’s in it for you as a scientist – you have many demands on your time. You want to do science and you find yourself spending 90% of your time putting out fires and explaining to others what you already know. And chasing the almighty Dollar, Euro, Yen or Rupee with grants, grant, grants or [...]
Science in the 21st Century! August 5, 2013 - Welcome to Science in the 21st Century! Less Time – Less Money – Less Staff – More Complexity – Bigger Problems – Trickier Solutions – Fewer Funding Sources – Tighter Deadlines… The solution to this litany of concerns is also the new paradigm for science – the distributed future – a world where collaboration rules and [...]
5th CDD Users and Community meeting – Registration open! July 30, 2013 - To celebrate our “10 Years of Collaborative Drug Discovery” we will host our CDD users and community meeting at the UCSF Mission Bay conference center in San Francisco on April 4th, 2014.
WIIFY Part 2 – Modern Drug Discovery Tools for Startup, Small Biotech, or Academics July 23, 2013 - What’s in it for you as the lab manager – the one ultimately responsible for results and funding? All it takes is one paradigm-shifting experiment or compound to validate your whole approach. You have an interesting hypothesis that’s why you are raising all the money and doing all these experiments. You have a hunch this [...]
Orphagen CEO Scott Thacher, Ph.D. + Director of Chemistry Ruo Steensma, Ph.D. July 12, 2013 - "We had Excel sheets all over the place and data from different projects that were just separated in different folders and after a while," says Dr. Ruo Steensma, "It got to the point that it was just hard to manage. We chose CDD, and we’re really happy with the service and the cost and the way the database is evolving."
GSK Published Kinase Inhibitor Set (PKIS) Now Available in the CDD Vault July 8, 2013 - There has been a lot of buzz around the GSK Protein Kinase Inhibitor Set (PKIS).
As noted in Derek Lowe’s In the Pipeline blog, “The company has made 367 compounds available to any academic investigator working in the kinase field, as long as they make their results publicly available… So if you're in academia, and interested in kinase pathways, you absolutely need to take a look at this compound set."
CDD in Chemical & Engineering News June 26, 2013 - The June 24 Issue of Chemical & Engineering News (C&E News) discussed the benefits of using collaborative software within the drug discovery industry. The article highlighted the need to manage and share data between drug firms and the academic labs and CROs.
Around the all important topic of security, Michael Elliott (CEO at Atrium Research & Consulting) mentioned in the article "I would argue that cloud applications have better protection than most companies have behind their firewalls."
CDD Vault Update: Performance and Easier Report Customization June 21, 2013 - We are continuously working to improve the performance of your CDD Vault, although we almost never mention it here. After all, good performance should be something you can expect. We’re going to break that tradition with this release, since it includes a major infrastructure upgrade that we’ve had brewing for quite a while. CDD should [...]
Scott Myers, Ph.D., Director of Drug Discovery – NeurOp, Inc. June 19, 2013 - "I recall early on trying to understand what should I do if I’m interested in science, but I’m not interested in medicine so to speak, like, being a medical doctor. And I was reading some descriptions about pharmacology and then I realized that sounded pretty exciting and also fit what I really thought I would like to do. That took me to pharmacy school. And in pharmacy school, I really realized I was more interested in the research and so I went the research path… That was over 20 years ago. And between then and now (when I got this job at NeurOp) NeurOp was really what I always wanted to do. I think this level of the in-vitro pharmacology and evaluating novel molecules has always been my main interest."
CDD to attend ACS meeting in September 2013 June 19, 2013 - CDD’s CEO & President, Dr. Barry Bunin, will be presenting several talks and posters at the 246th National ACS meeting in Indianapolis from September 8th through 10th, 2013. Come visit us at Booth 1107 at the ACS Exposition between September 8th-10th, 2013, to witness the power and flexibility of CDD Vault. Two Talks: Pistoia Alliance and the emerging HELM standard [...]
WIIFY Part 1- Modern Drug Discovery Tools for Startup, Small Biotech, or Academics June 19, 2013 - What’s in it for startups, small biotechs or academic laboratories looking for great drug discovery tools…without the great, big price? When looking for important trends across multiple experiments, you can forget about using multiple excel files. You need to be able to see trends quickly, to wisely prioritize precious compounds, reagents, assays, and resources. You [...]
CDD Vault Update: Gargantuan Summer Update! May 31, 2013 - In this colossal release we introduce e-mail alerts, reference compound controls with plot overlays, an improved run summary for quality control, and new site navigation. E-mail Alerts Now you can automatically be notified when new results are added to CDD. These alerts are fully configurable, so you have control over the types of events that [...]
How you move compounds may matter May 6, 2013 - Dispensing Processes Impact Apparent Biological Activity From the desk of Sean Ekins, VP Science, Collaborative Drug Discovery, Inc. I have several collaborations that are well outside my CDD role and one of these may be of broader interest to CDD users. A recent PLOS ONE article “Dispensing Processes Impact Apparent Biological Activity as Determined by [...]
Trending Now – Collaborative Technology! April 26, 2013 - The New Trend in Science – Collaborative Technology! Collaborative technology has been in place for a decade, yet the trend towards collaboration is only now becoming a hot topic. David Raths article in KM World “Knowledge-sharing platforms emerge from life science research collaboration” provides a plethora of examples for this. Established companies likeCollaborative Drug Discovery have [...]
CDD to Present at World Malaria Day Event April 23, 2013 - 
CDD will be presenting a talk and two posters at a Zagaya World Malaria Day Event this Thursday (April 25) in Emeryville. Although the case studies and examples are for Malaria, it is worth noting that the CDD Vault technology is "therapeutic area agnostic" and thus equally applicable to commercial applications. Here is the full program...
CDD Vault Update: Write API April 19, 2013 - This release rounds out CDD’s Application Programming Interface (API). With fine-grained write access to molecule and batch objects, the API now provides bi-directional communication between the CDD Vault and your other tools. Link your ELN directly to the CDD Vault, combining the flexibility of ELN reaction capture with the SAR tables and search capability of [...]
Elsevier Acquisition of Mendeley by Mendelspod Plugs CDD April 17, 2013 - Theral Timpson had a humorous blog about open science in light of the Elsevier acquisition of Mendeley.
The funniest quote from one commenter compared it to "Haliburton buying Green Peace."
In his article, there was a concise description of how CDD spans the commercial private and external domains required for drug discovery IP...
Among the many valuable resources available at ChEMBL is the Kinase SARfari subset. To make this data available in the CDD interface, we took the core table of Kinase SARfari and merged it with another key table from the ChEMBL database, providing a field describing the assay utilized in each record in much greater detail than is available in native SARfari. We have now made this merged dataset available via the CDD interface. In this new dataset, we have created 400 protocols, where each protocol represents one of the 400 kinases in the SARfari database. This organization allows users to search by molecule, substructure, kinase target, or assay result. This allows one to... 
CDD Vault Update: Prêt à importer April 3, 2013 - Prêt à importer Have you ever tried to start an import, only to find the vault locked by another user’s import? Well, no more! Now your vault is always ready to import! Map And Queue Imports At Any Time You can now map and queue imports at any time, regardless of other imports in progress. [...]
Happy Birthday CDD! April 1, 2013 - “Happy Birthday to you, happy birthday to you, happy birthday dear C-D-D… happy birthday to you.” CDD was founded in April 2004, spun out of Lilly – a little bundle in the cradle then, and…. oh boy….did that kid grow up fast! It was a bit a disruptive, revolutionary child….how so? Let’s look back for [...]
World TB Day 2013 March 24, 2013 - From the desk of Sean Ekins (VP Science) It’s World TB day 2013 and each year we try to put a few words together to raise awareness and highlight recent development. In recent months we have seen a new therapy for TB-MDR approved in bedaquiline. And yet still we need faster cures to battle this [...]
Trypanosomal Inhibitors via Target Class Repurposing Profiled March 8, 2013 - 
The most recent data set profiled on CDD Public, called “PARASITES: Inhibitors via Target Class Repurposing”, comes from Mike Pollastri's laboratory at NEU. In this guest-blog post, Mike talks about his publications and data. Our laboratory at Northeastern University collaborates with several parasitology groups around the world, performing neglected disease drug discovery. This shared data set contains the biochemical and cellular screening data for our published work applying the target class repurposing approach. Currently, the published data sets include trypanosomal phosphpodiesterase (TbrPDEB1 and B2) inhibitor... 
CDD at New Orleans National ACS Meeting February 27, 2013 - CDD will be at Booth 205 (in the back by concessions) and VP of Science Dr. Sean Ekins will be giving 8 (eight) presentations at the New Orleans National ACS meeting from April 7 - 11th...
Informatics Considerations at the Dawn of the Antibody Drug Conjugate Era February 25, 2013 - Congratulations to Genentech/Roche-ImmunoGen on the FDA Approval of Kadcyla (Ado-Trastuzumab Emtansine), an Antibody-Drug Conjugate for Her2-Positive Metastatic Breast Cancer Antibody-Drug Conjugates (ADCs) combine the best of Nature’s capacity to rapidly evolve specificity with Science’s capacity to deliver specifically designed functionality. There are fascinating, unique ADC SAR (Structure Activity Relationship) informatics representation and optimization challenges when [...]
From CDD Vault to the TB Mobile app: helping Tuberculosis researchers February 19, 2013 - Guest blog by Dr. Alex M. Clark, Molecular Materials Informatics, Inc. What do you get when you combine a company with an online collaborative chemistry sharing platform, a startup dedicated to producing cutting edge apps for chemistry, a consultant with deep domain knowledge and lots of ideas, a researcher with access to valuable data, and [...]
Be Our Valentine at the TriConference Feb 14th in San Francisco February 1, 2013 - “If you’re going to San Francisco, be sure to wear some flowers in your hair” Feb 13-14th, CDD will be in force at the Moscone Center in San Francisco for the MMM Triconference at Booth #506 (to your right after entering the Exhibit Hall by the food and beverages, you can register for the Exhibit [...]
CDD Vault Update: Batch Fields, aka Configurable Registration Rules February 1, 2013 - CDD’s BFs are here. Despite the pop-culture “best friends” acronym, BF stands for Batch Fields, but we feel that they will become your best friends soon enough! Batch fields allow for customization of molecule registration rules to suit each vault’s needs. They apply to vaults with and without formal chemical registration, and are fully integrated [...]
CDD’s TBDA Collaboration with BMGF, Glaxo’s “Open Lab” & half-a-dozen Big Pharmas Highlighted in the Economist January 23, 2013 - The Economist's Jan 12 Schumpeter series on world business trends highlighted the Gates Foundation collaboration with academics, non-profit, and government laboratories with 7 big pharmas! 
Four new public data collections to support drug discovery for Chagas disease January 17, 2013 - Chagas disease is a silent and slow killer. Children in poor, rural areas of Latin America are commonly bit by “kissing bugs” and infected with a parasite called Trypanosoma cruzi. During the initial infection, most children have only mild symptoms and recover without treatment. Unfortunately, in many cases the parasite is not really gone, it’s [...]
Bedaquiline approved by FDA January 14, 2013 - The first Tuberculosis drug in 40 years! The FDA just last week approved the first new treatment for tuberculosis in 40 years, Bedaquiline (also known as Sirturo, TMC207 or R207910). This drug was discovered via the screening of 70,000 compounds for activity against M smegmatis, a more rapidly growing and manageable mycobacterium compared with M. [...]
Collaboration is here to stay – 2012 CDD Holiday Poem December 4, 2012 - 
Collaboration is here to stay
Collaborate this holiday
Kiss a drug – with a gene
Hug the target, in between
Year end budget, always lean
...
(TMC-207) was backed by the FDA panel that has been reviewing it since late June. Hopefully it will be approved by the FDA in due course because then it becomes the first drug approved for tuberculosis in well over 40 years. While this is terrific news for patients, we need additional molecules in the pipeline because elevated liver enzymes and QT prolongation were observed...
Crowdsourced Funding for Scientific Experiments November 29, 2012 - Congratulations to Dr. Ethan Perlstein at Princeton. In addition to doing innovative science, he has been innovating on aspects of science touching the Internet and Funding. His lab raised over $25,000 on the crowdfunding site RocketHub for their basic research project. Ethan and his collaborators at Columbia are studying the subcellular distribution of radioactive amphetamines [...]
Michael Siani-Rose Brings Diverse Talents to CDD November 27, 2012 - Mr. Michael Siani-Rose brings his successful track record at Affymetrix, Chiron, Kosan, and Gryphon to CDD. Michael Siani-Rose (CDD Informatics) was most recently President of Cell Therapy Company Theregen. Of particular relevance for CDD, with the emergence of Antibody Drug Conjugates and informatics standards such as HELM from big pharmas, Michael Siani-Rose co-published with SMILES [...]
CDD’s software architecture advantage, part III November 27, 2012 - 
Other lessons we learned at CDD from running our multitenant system since 2004:
The CDD Vault as a multitenant architecture evolved based on the user community’s feedback and real needs. 
CDD Vault Update: Say Hello to the New API November 20, 2012 - For those of you that have been eagerly awaiting a way to connect your CDD data repository to other applications— the beta version of the API is here for your testing and coding pleasure! In addition to the Application Programming Interface, we’ve also updated the search results display and the handling of units of measurement. [...]
2012 Drug Repositioning Conference Highlights November 8, 2012 - 
The second annual Drug Repositioning and Indications Discovery Conference was held again in the San Francisco Bay Area on Oct 23-24, and similar to last year, Dr. Barry Bunin chaired an exciting panel discussion. Perhaps co-hosting this Drug Repositioning Summit will become an annual tradition for CDD!
This year's distinguished panelists included Dr. Christine Colvis, Dr. Christopher Lipinski, and Dr. David Cavalla.
Drug Discovery Informatics Veteran Joins CDD November 5, 2012 - Dr. Michael Travers brings a reproducible track record of commercially successful, informatics innovation to CDD’s strong technical team. Dr. Travers’ broad bioinformatics and chemoinformatics experience adds an eclectic wind to CDD’s sail. Dr. Michael Travers (CDD Software Design) hails from SRI International’s Bioinformatics Research Group, where he worked on developing software tools to support [...]
Using the CDD Vault as collaborative lab inventory system – an example October 26, 2012 - 
Three years ago the Martin research group at the University of Texas, Austin worked with Collaborative Drug Discovery to establish and maintain a chemical inventory for over 3,000 compounds. This online inventory application is easy to set up, maintain, and use.
CDD’s software architecture advantage, part II October 24, 2012 - 
Software evolves rapidly. We all get updates and upgrades of operating systems, bug fixes, security patches, new security software, new features at an ever faster pace. This is a big plus for customers of a multitenant application because all of the updates, latest security features, and new functionalities can be implemented quickly without interfering with each client’s implementation.
Rare Disease Challenge – Be HEARD October 19, 2012 - 
Assay Depot and Rare Genomics Institute Unite 19 Life Science Companies to Launch a Rare Disease Research Competition. We at CDD are proud to be part of the Open Science Challenge with Assay Depot.
Introducing TB Mobile October 16, 2012 - 
At CDD, we are focused on novel strategies for developing inhibitors of Mycobacterium tuberculosis (Mtb) as tuberculosis (TB) drugs. Tuberculosis kills 1.8 million people every year (~1 every 8 seconds). We are introducing TB Mobile that displays molecule structure and links to the bioinformatics data on >700 molecules screened versus Mtb and their targets.
CDD Vault Update: Smörgåsbord! October 12, 2012 - This release has something for everyone, from project managers to vault admins, and from informaticians to lab techs. Dashboard Reports As a project manager or a lab’s PI, you want a quick summary of your group’s progress. One click away from the Dashboard is the new Reports tab, which shows your team’s productivity over the [...]
Dr. David Matthews, Pathway Therapeutics, Vice President, Drug Discovery and Exploratory Development October 10, 2012 - "So I actually started out life as a physicist. My undergraduate degree was physics and during that time my undergraduate tutor was Professor David Blow, who was at Imperial College where I did my degree. He was one of the pioneers of x-ray crystallography, sadly passed away a few years ago, but I would say that David was certainly instrumental in fostering my interest in biology and as I went through my undergraduate degree, I realized that this was a field that was fascinating to me, that I really wanted to get into. So I guess that would be the first turning point was in making the decision to mutate from a physicist into a biologist."
Collaboration, GrantStorming, and You – Oh My! October 7, 2012 - 
I recently had the pleasure of discussing the parallels between art and science with Theral Timpson at Mendelspod.
Around eight minutes into the interview, I described how web-based software is art. And taken as a whole, the Internet is arguably humanity's greatest collaborative work of art.
What's the pragmatic relevance for busy drug discovery scientists and business people...
CDD Welcomes Charlie Weatherall to Scale Accounts Management September 28, 2012 - Press release BURLINGAME, Calif., 27 Sept 2012 — Collaborative Drug Discovery (CDD) announces the addition of Charlie Weatherall to magnify CDD’s focus on its Community, further promoting the widespread acceptance of CDD’s platform among academic, government, biotech and pharma researchers. Prior to joining CDD, Charlie Weatherall worked with industry-leading scientific software companies such as MDL (dating [...]
CDD’s software architecture advantage, part I of III September 20, 2012 - 
There is a heated debate in information technology regarding whether single tenant or multitenant applications are the way to go. What is the “real cloud” vs. “private cloud” (or “fake cloud” as Marc Benioff, CEO and founder of Salesforce.com, calls it)? This debate has spilled over into drug discovery informatics. Let’s explore the differences and then discuss the pros and cons for both options.
Molecular Medicine Triconference 2013 in San Francisco September 11, 2012 - Dr. Barry Bunin will Present and Chair the "Collaboration and Externalization" at the 5th Annual Integrated R&D Informatics & Knowledge Management Channel.
P.S. By popular demand, CDD will be doing our one cool SmartBoard to CDD Larger than Life at the exhibit (Booth #506) right by the ice cream...and we'll be handing out the equally popular Baby CDD Onesies (for if you or anyone you know was ever a baby:).
CDD Vault Update: Escape from the Dose-Response Thicket September 6, 2012 - Before we introduce our next major feature release, here is a collection of small but helpful changes to CDD. Escape from the Dose-Response Thicket When a compound has been assayed many times, its dose-response plot can become an impenetrable thicket of curves. As of this release we only show the curves that match your search [...]
Eric Springman, Ph.D., Celtaxsys CSO August 30, 2012 - "It’s just amazing how science comes and goes in waves. Some of that is related to the tools that you have at your disposal, but when I started out in discovery science and my graduate work and post-doc, particularly the innate immune system, but neutrophils, and this is where I dwell right now, so it’s pretty fascinating to me how it’s coming around. Neutrophils were just viewed as pretty unsophisticated dumb cells in that they were, as we called them, terminally differentiated, which had a lot of implications to it, that they just basically couldn’t think anymore as cells think, they were just preprogrammed to do something and then die. And that really has turned around on its head to where even the cells that we have thought of for a long time now, for the last 20 years as primitive, are actually not at all, they’re very sophisticated cells."
Mendeley-CDD Barry Bunin Interview August 20, 2012 - 
There is a growing ecosystem of collaborative tools for doing science, CDD's Barry Bunin spoke with our colleagues at Mendeley about CDD's role in the ecosystem, his vision for the brighter future and everything in between. Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research.
CDD Vault Update: Collections Polish August 17, 2012 - With this release, we are polishing up molecule collections by adding two nice cherries on the top! Explore Imported Data You can now see all registered molecules and associated protocol data from a single imported file with one click. Once a data import is committed, click on the “Explore imported data” link to see the [...]
CDD Announces $1M Phase 2 STTR Grant with SRI International August 16, 2012 - 
Collaborative Drug Discovery (CDD) is in a unique position for drug discovery grants because of the CDD business model precluding ownership of Drug Discovery IP, as well as the complementary chemoinformatics and collaborative web-software capabilities.
Because of the heterogeneity of biological therapeutic areas, targets, hypotheses, and screens, together with the increasing importance of informatics and collaboration, the door is now open for numerous similar at a meta-level, yet completely different and novel in the specific collaborations. Directly contact CDD CEO Barry Bunin for ideas on projects that could benefit from a collaborative, data driven approach to take “good ideas to great”.
CDD Vault Update: 1536 wells of happiness August 8, 2012 - We interrupt our regularly scheduled releases to announce 1536-well plate support. We just couldn’t wait. Import your plate data and CDD will automatically assign the correct plate size: 96, 384, or 1536-well. The new size is fully supported, including molecule plates maps, control layouts and data normalization, heat-map visualization and plate scatter plots with control [...]
Migrating legacy biological and chemical data into the CDD Vault August 7, 2012 - 
If you have an old drug discovery informatics system and it is full with data – but the system is not well maintained or supported any more or too expensive for your budget, then you have a good reason to get new data management software.
You may however be really concerned about the change because you don’t know what to expect. 
Q: How do you see CDD evolving over the next couple years? A: I think it’ll grow wings and fly. August 3, 2012 - 
Barry Bunin talked to Science Exchange about how CDD got started, what it is, and where it's going. Science Exchange is a community marketplace for scientists and the easiest way to get experiments conducted by researchers in top core facilities and institutions.
This press release came in yesterday and we thought that this is so exciting that we wanted to blog about it. Congratulations to both, Assay Depot and to Astra Zeneca!
Why are we at CDD getting so excited about this particular news? Because Virtual Research is the future and some companies are not just talking about it but actually doing something for real commercial projects like this one.
Congratulations to Onyx Pharmaceuticals! July 24, 2012 - 
Congratulations to Onyx Pharmaceuticals on the accelerated FDA approval of Kyprolis™ (carfilzomib) for Injection, a proteasome inhibitor for the treatment of patients with multiple myeloma.
Read the official press release.
What’s the antidote for big data pains at HTS Core Facilities? July 23, 2012 - 
Originally a province of the pharmaceutical industry, drug discovery has become firmly entrenched in the academic domain in the recent years too. Operating on a smaller scale than in pharma, academic and non-profit drug discovery has become possible with High Throughput Screening (HTS) Core facilities within the university.
Traditionally, most universities share many types of Cores, such as animal facilities, mass spectrometry, and the like, and now the need for HTS cores has become a priority. The clients of such facilities are typically basic biology and chemistry investigators who have the funding, but lack the necessary technical expertise or instrumentation to fulfill their research needs.
CDD in TB Biomedical Computation Review July 20, 2012 - CDD's TB drug discovery collaborations spearheaded by Dr. Sean Ekins were included in Katharine Miller's Biomedical Computation Review Article titled:
"Where Tuberculosis Meets Computation: 10 Points of Intersection, How computation offers a window into a disease often described as a black box."
Quite a Catch! July 16, 2012 - 
In June 2012, Phil Crews, Distinguished Professor of Chemistry at the University of California, Santa Cruz, delivered his last official “Introduction to Organic Chemistry” lecture after 42 years of teaching. Literally thousands of students have benefited from his dedication to education! This retirement from academia is only partial as he plans to continue his research in chemistry of marine natural products that began in 1974 after perusing a book entitled Poisonous and Venomous Marine Animals of the World. From this book he learned that extracts from sponges exhibit antibiotic and anti-parasitic properties but their chemistry is largely unknown. His imagination captivated, he decided to embark on the adventurous research path at UCSC that continues to be highly productive nearly forty years later.
Virtual Pharma, Externalization, FIPnet, VIPCO – like gravity, you can fight it but you will lose (Part 4 – Scalability) July 16, 2012 - 
Support is different with CDD. And it comes down to economics. Traditional database and ELN solutions have required high support costs - often with staff on site and costs as high or higher than the purchased technology.
CDD from day one has supported globally distributed groups via the web and phone. In this regard, a large academic user base is particularly noteworthy. An old joke among Vendors is that academics (due to their highly independent nature and budgets) traditionally require twice the support for half the budget. One needs to be 4x more efficient to really effectively support this marketplace. Yet CDD has thrived with users in the academic community.
Virtual Pharma, Externalization, FIPNet, VIPCO – like gravity, you can fight it but you will lose (Part 3 – Partitioning) July 3, 2012 - 
Collaborative - flexible, facile, secure data partitioning
To really support the virtual model and externalization, the technology must be collaborative, with data partitioning designed into the application. Optimally the technology is 100% in the Cloud (unless folks are intentionally trying to be more expensive).
How to do more with less = Science Exchange + existing expert academic capacity June 30, 2012 - 
At CDD we keep a close eye on the space where science, technology and collaboration meet. In this context we want to introduce “Science Exchange” to you, our user community. Barry Bunin (our CEO) met Elizabeth Iorns, the CEO and founder of Science Exchange at the Science Startup Conference
.
Virtual Pharma, Externalization, FIPNet, VIPCO – like gravity, you can fight it, but you’ll lose (Part 2 – Simplicity) June 26, 2012 - 
CDD's byline "Archive, Mine, Collaborate" has "Archive" as the foundation. Through an intuitive graphical user interface (GUI), configurable data space, intelligent mapping algorithms, and saved templates, CDD significantly lowers the activation energy for data archival, and therefore compliance on the part of the end-users. How many people have you met that get excited by data entry?!
Virtual Pharma, Externalization, FIPNet, VIPCO – like gravity, you can fight it, but you’ll lose (Part 1) June 21, 2012 - 
Yesterday's expensive FIPCO (Fully Integrated Pharmaceutical Company) model has been replaced with today's FIPNet (Fully Integrated Pharmaceutical Network) aka VIPCO (Virtually Integrated Pharmaceutical Company) models. What does this really mean? What are the pitfalls when implemented poorly? What is the potential upside? Which people and technologies will win in this new environment?
CDD Vault Update: More Collections and Detail Pages Cleanup June 20, 2012 - This release introduces some additional Collections goodies as well as few usability enhancements for the the molecule, protocol, run, and plate details pages. Collections Intersection You can now search for all molecules that are in two or more collections (AND). New Collections Tab on Molecule Page Here you can see the collections that include this [...]
Collaboration as the key to turning around the drug discovery business (Part 12) June 18, 2012 - 
Ubuntu is defined by Wikipedia as "an African ethic or humanist philosophy focusing on people's allegiances and relations with each other." The idea is that we become richer and derive meaning specifically (even primarily) via our interactions with others. Richer personally. What does Ubuntu have to do with modern technology, business, economics, and drug discovery?
Dr. Joel Freundlich, UMDNJ June 12, 2012 - "When you see that activity in a mouse model with the compound that you designed and made and ushered through those early stages, that's really, really exciting... We use CDD Vault all the time for programs where we are evolving structure activity relationships, understanding how a small molecule modulates the target. We are able to track those changes in both graphical and numerical ways seeing how structure influences inhibition of a target. That is just incredibly valuable to us, together with the ability to share the information amongst many different collaborators whom I'm really privileged to have. It is extremely important to exchange data in a seamless fashion. And there is the immense amount of public data that's been archived on CDD Vault."
Is it really that easy to find a new inexpensive drug? May 22, 2012 - 
A team of Collaborators in the CDD network from UCSF, working with Professor McKerrow, and UCSD, working with Professor Reed, discovered that - the main cause for human dysentery.
CDD Vault Update: Molecule Collections May 21, 2012 - Have you ever wished CDD tracked your lead molecules or allowed you to restrict searches using a list of molecules or even combinations of lists? Wish no more: we are introducing molecule collections. With this first release, you can create collections and search using one collection at a time. Even better, the next 3 releases [...]
Too big to … “go cloud”? May 15, 2012 - 
This article here: Cloud is a corporate strategy, not a tactical solution resonated because I see this occasionally with those who have the luxury of IT departments and large existing IT/IS infrastructure.
Collaboration as the key to turning around the drug discovery business (Part 11) – The future May 11, 2012 - The prerequisite to enable the efficiencies of integrated specialization, are secure, trusted collaborative platforms. Mechanisms are required that balance allowing maximum collective contributions, with maximum control of intellectual property ownership. Fortunately, technologies are emerging in this area to allow what was previously impossible, to become routine. Platforms like LinkedIn and Facebook, with rich, flexible [...]
The Collaborative Discovery of a new subatomic particle April 28, 2012 - 
The CMS collaboration described the first observation of an excited, neutral Xi_b baryon, a particle made up of three quarks, including one beauty quark.
Although the key experiments took place at the CERN Large Hadron Collider, researchers from all over the world participated intellectually. The drug discovery community is poised to reap the same benefits by watching how the forward-leaning physics community embraces the growing importance of internet accelerated scientific collaboration.
Collaboration as the key to turning around the drug discovery business (Part 10) – Learning from eBay, NASDAQ, Airlines, & Hollywood April 25, 2012 - 
Airline businesses provide an economic multiplier effect for all users that greatly exceeds the margins of the airlines. Many airlines have little to no margins, but it is hard to imagine a modern society without convenient air travel today.
In Hollywood, typically 3 or more partners work together to bring a visionary blockbuster to market, in contrast to the historical approach for blockbuster drugs.
For our industry, the key emerging question is how can consortia of industry, academia, foundation, and government intellectual property guardians evolve a mechanism that allows similar efficiencies in drug discovery?
CDD Vault Update: Spring Cleaning Release #3 April 23, 2012 - For this third installment, we introduce the highly coveted ability to edit salt data for batches, and a simplified workflow for registering new batches in registration vaults. Other enhancements include a standard deviation calculation for averaged data, as well as a black and white printing option for structure images. Simplified Batch Registration (For vaults that [...]
Stephen Bergmeier: From Shoebox to the Cloud, Collaboration Then and Now April 19, 2012 - "…I have sitting on my desk a shoe box kind of box and it’s got little four by six file cards and on each one of these four by six file cards I have a structure drawn and it’s got a compound identifier and we have someone’s name on there as the person who made the compound and on the various cards there are sort of little pencil marks indicating that we sent so much of it to somebody or we looked at it in a particular assay. And so, you know, actually this is another one of the reasons I really like CDD Vault, is I’m getting rid of my shoeboxes of file cards."
CDD Vault Update: Spring Cleaning Release #2 April 6, 2012 - This second installment of our Spring Cleaning series brings you two highly requested enhancements. Read on! Exact Keyword Search By default, molecule keyword searches now return results that match your terms exactly. This allows you to find a precise list of molecules using molecule names, user-defined fields, or any other combination of keywords. Of course, [...]
Open, Collaborative, & Private Data April 3, 2012 - Welcome to the Party! CDD has supported the complementary virtues of public with private sensitive drug discovery data since the Oct 26th, 2007 publication of “1721 FDA approved drugs with designated indications, sponsor name, and chemical structures” with Dr. Christopher Lipinski. To emphasize the security and privacy, even on a subconscious level, the platform [...]
CDD – 8 years in the cloud. Really. April 1, 2012 - Our cloud based drug discovery software celebrates its 8th birthday From the desk of Sylvia Ernst – CDD Sr. Director Community Growth Yes – it is April 1st – and yes – it is true. CDD was founded on April 1st 2004 and started running a web-based database to join molecules with their many bioassay data. [...]
CDD Vault Update: Spring Cleaning Release #1 March 30, 2012 - Instead of adding the next major feature, we’re pausing for a moment to polish the existing application and implement your most commonly requested small changes. This is the first in a series of releases intended to make your day-to-day experience with CDD more enjoyable. Dose-Response: Better axes and labels X-axis labels now show concentration [...]
World TB Day 2012 March 24, 2012 - From the desk of Dr. Barry A. Bunin – CEO, Collaborative Drug Discovery (CDD): Raise awareness, overcome resistance, shorten treatment, optimize drugs to minimize the future human toll from Tuberculosis this World TB Day 2012. I wish it were not true, but unfortunately, last year’s blog on World TB Day 2011 by Dr. Sean [...]
Why you need to stop meeting in-person now for doing business! March 22, 2012 - Work 3.0 is here and competing with you! From the desk of Sylvia Ernst, Ph.D – Sr. Director Community Growth at CDD Just recently LinkedIn featured this article: http://www.inc.com/rene-siegel/five-reasons-you-need-to-meet-in-person.html and it got raving comments. But let’s think this through for a moment. I would counter that in person meetings – and a corporate culture [...]
CDD Vault Update: Normalize Dose-Response Data? Yes We Can! March 16, 2012 - With this highly anticipated release, you can start importing raw data for your dose-response experiments, and let CDD calculate % activity based on controls. This is building on existing functionality of calculating EC50 based on % activity. We hope you will be able to import dose-response data into CDD as they are generated, eliminating the [...]
Collaboration as the key to turning around the drug discovery business (Part 9) – Collaborate better March 13, 2012 - Collaboration as the key to turning around the drug discovery business (Part 9) - Collaborate better.
New insights into the nature of creativity emphasize the value of interacting with different people with different ideas for non-linear breakthroughs.
Why you can’t avoid the “web” any longer for your Drug Discovery data March 8, 2012 - Surfing two disruptive waves: “The Cloud” and “Collaboration” From the desk of Sylvia Ernst – CDD Sr. Director Community Growth Remember those days? A while ago the computing world changed from Terminal/Host systems to Client-Server technology; that was in the early nineties. Terminal/Host required an expert for data input into a terminal and the data were processed [...]
Collaborative (Rare Disease) Drug Discovery Day March 1, 2012 - Today is Rare Disease Day. In a way, every day for CDD and the CDD community is Rare Disease Day. Why? Effective collaborations are the key to efficient drug discovery on a tight budget. And by definition, all rare disease drug discovery must be done on a tight budget leveraging a small number of [...]
CDD Vault Update: À la Carte Commit for Data Import February 29, 2012 - This release introduces the ability to selectively reject/accept all events of a specific type. Sometimes, a data import can have some unexpected (and undesired) consequences. Before today, if you wanted to prevent those consequences, your only choice was to cancel the import, correct the file and re-upload. This was fine if you were only dealing [...]
Dr. Michael Pollastri, Northeastern University February 15, 2012 - "…being able to basically have a one-stop shop for people in my group to go and actually look for their data across multiple projects and also to have my collaborators to be able to just sort of access in an easy way the data that’s relevant to their projects without making it a really sort of arduous search to do. I mean basically it’s almost like the Project’s concept was designed for projects – for labs like mine."
Collaboration as the key to turning around the drug discovery business (Part 8) – Standards February 14, 2012 - Collaborative drug discovery platforms are broadly applicable across therapeutic areas, targets, and teams. All drug discovery projects have numerous conserved technical and commercialization hurdles. The regulatory, scientific, and economic foundations of drug development are conserved. Apart from the fascinating, idiosyncratic manifestations arising from different molecules, targets, assays, and teams…there are common, systematic technical challenges [...]
A More Enlightened Approach to ADME? January 27, 2012 - Animals as surrogate test subjects for humans are becoming less desirable as the effects of cost, negative social pressure, and the reality that animals are not always accurate predictors of human outcome move research to consider alternatives. 
Finding a cure for TB: The world is a virtual lab and the cloud is the limit! January 14, 2012 - From the desk of Sylvia Ernst, Ph.D – Sr. Director Community Growth at CDD Neglected disease research is one of our passions here at CDD – Malaria and TB in particular. Yesterday, I (Sylvia Ernst) came across this well written Wired Magazine Article that references back to a related recent Times of India Article on TDR (Totally [...]
Collaboration as the key to turning around the drug discovery business (Part 6) – Technology can make things easier January 4, 2012 - Science is hard. Drug Discovery is hard. Chemistry is hard. Biology is hard. Business is hard. Innovation is hard. Management is hard. Technology can make things easier. Some technologies make a little impact. Other technologies, such as the printing press in years past and the linking of computers via the Internet more recently, have [...]
CDD Vault Update: Enhanced Security Options December 18, 2011 - Two-Factor Authentication In this release CDD introduces an optional second layer of user authentication for groups that prefer added security. While a strong password is sufficient for most groups, a Vault can now require a second authentication step via mobile device or telephone. CDD has partnered with Duo Security (www.duosecurity.com) to deliver this free option, [...]
The beginning of the end of AIDS December 15, 2011 - The CDD community works on web-catalyzed scientific breakthroughs to accelerate drug discovery for global human health. For AIDS eradication the challenge is social as much as scientific. Antiviral treatments are available and recently studies suggest they are even preventative. A small one-time investment will save lives and significant money long term. As a race, we [...]
Malcolm Kendall (President & CEO), Indel Therapeutics, Inc. December 9, 2011 - "CDD Vault is a G=d-send. We are a virtual company. I’ve got people spread from Montreal to Vancouver to L.A. and we really needed some way to kind of bring it all together and capture the data that we were creating and be able to share and analyze it. So it’s become sort of a critical part of our existence, in a sense. Before we were capturing data on spreadsheets so having a web-served application like CDD Vault, allows you to collaborate real-time with your people, spread across two countries and several time zones. It is easy to use, has lots of features and because of it we can now better use and share the data we are creating."
Congratulations to Researchers from Onyx, Proteolix, Yale, and Cal Tech on the FDA Acceptance of the New Drug Application for Carfilzomib for Multiple Myeloma December 1, 2011 - Onyx announced that the U.S. Food and Drug Administration (FDA) has accepted the New Drug Application (NDA) submission for carfilzomib, a next generation proteasome inhibitor, for the potential treatment of patients with relapsed and refractory multiple myeloma. The drug candidate was developed by Proteolix which in licensed the initial discovery from academic researchers at [...]
New data released: Trypanosomal phosphodiesterase inhibitors. November 10, 2011 - A new public data set has been released from the neglected disease drug discovery team at Northeastern University (Boston, MA) and the Marine Biological Laboratory at Woods Hole, as reported in the Journal of Medicinal Chemistry this week (DOI: 10.1021/jm201148s). This data set consists of a range of established human phosphodiesterase inhibitors, tested for inhibition [...]
CDD Vault Update: Collaboration Privacy: Vault Member Names October 21, 2011 - Collaboration Privacy: Vault Member Names While project data has and always will be secure, we are increasing privacy for Vaults that hinge on keeping their collaborator’s names hidden. The enhanced privacy should allow each Vault to invite every single collaborator working on a particular project to CDD. This way, everyone can take advantage of the [...]
5 Reasons Why Collaborative Scientists Use CDD October 17, 2011 - CDD provides Projects inside secure CDD Vaults™ for temporal, spatial, and data-type partitioning capabilities whether it is for a single shared compound or HTS screening campaign. CDD’s lightweight chemical registration and SAR technology and services are economical for those in budget conscious labs to large pharmaceutical companies. CDD supports collaborations from the single lab to [...]
Accelrys Shines a Spotlight on CDD in BioIT World October 17, 2011 - Per the recent write-up by Kevin Davies in BioIT World, we welcome industry leader Accelrys (with many very different products under their umbrella) to the collaborative SAAS space we’ve been focused on for over 7 years. CDD Projects right in collaborative CDD Vaults let you easily collaborate in your natural workflows – no multiple [...]
CDD Vault Update: Importing Data: More Noteworthy Events October 11, 2011 - Importing Data: More Noteworthy Events We’ve fallen in love with the new data import summary, particularly how it reveals exactly what events will occur. It does such a good job of being clear and revealing that it highlighted some cases where we weren’t reporting noteworthy events. This release addresses that, along with many other small [...]
Dr. Thomas J. Magliery, Ohio State University September 27, 2011 - Thomas J. Magliery was born in Oak Park, Illinois, in 1974 and grew up outside of Chicago and Indianapolis. He conducted medical genetics research with M. Ed Hodes at the Indiana University Medical Center in Indianapolis, leading to a semifinalist-winning project in the Westinghouse Science Search in 1992. Fast-forward a few years at Berkeley, Scripps and Yale, and Dr. Magliery joins the faculty of the Ohio State University in the fall of 2005 as an Assistant Professor in the Department of Chemistry and the Department of Biochemistry. He is a member of the Ohio State Biochemistry Program, the Biophysics Graduate Program and the Chemistry-Biology Interface Training Program.
CDD Vault Update: A Single-Page QC Report September 23, 2011 - The most critical decision you have to make when importing data in CDD is whether you should commit the data or not. The previous version of the report gave you access to all the information but it did a bad job highlighting the important facts that should drive your decision. The new single-page report groups [...]
CDD’s Sean Ekins Elected to Pistoia Alliance BOD September 15, 2011 - Following recent blogs and provocative conversations regarding the Pistoia Alliance we are proud to announce that CDD’s very own Collaborations Director, Dr. Sean Ekins, was recently voted onto the BOD for this organization. We look forward to assisting in the future success of Pistoia and promoting some of the initiatives we have described and believe [...]
What’s wrong with the Pistoia Alliance…and why we’re renewing our annual membership! (Part 1) August 31, 2011 - Pistoia folks have the right attitude (precompetitive work to avoid redundancy), use the right tools (Basecamp), but don’t go nearly far enough. Although clothed in novelty and open mindedness, it is essentially the same vendors and embracing the same approaches, with evolutionary, not revolutionary, advances. The Pistoia Alliance correctly points out the problems in their [...]
CDD Vault Update: Importing Data with a Simpler Mapper (That Does More) August 22, 2011 - You can now provide default values when importing data by adding virtual fields to your file. This change allowed us to remove the bulky Default Values section, presenting a cleaner interface to all users while preserving and expanding advanced functionality. Easily Add Missing Fields To add a default value for every record in your file, [...]
Collaboration as the key to turning around the drug discovery business (Part 4) – Collaboration and Innovation August 18, 2011 - What is the right type of innovation for successful drug discovery today? How do innovation and collaboration contribute to the success of your drug discovery efforts today? The answers depend upon your strengths, weakness, opportunities and threats (SWOT analysis). As much as there is no single formula for all situations, there are more and less [...]
Congratulations to researchers from Plexxikon and Genentech on the FDA Approval of Zelboraf – an oral, small molecule kinase inhibitor for skin cancer August 18, 2011 - Congratulations to researchers from Plexxikon (now Daiichi Sankyo) and Genentech on the FDA Approval of Zelboraf – an oral, small molecule kinase inhibitor for skin cancer! For all the bad news we read, it is important as a community that we celebrate our scientific and business triumphs. Innovation matters. Here are the exciting results of [...]
Dr. Barry Bunin, CDD's founder and CEO, recently gave an interview for FounderLY. In this 2-part interview, he shares his background, how CDD came to be and what drives us.
E.T. phone home August 7, 2011 - NASA scientists found both terrestrial and extraterrestrial nucleotides on meteors in the Antarctic and Australia. The experiments were performed with minimal risk of earthly contaminants. Perhaps, per the immortal words of Joni Mitchell, “we are star dust” after all. Maybe biologists and chemists have underestimated the likelihood elsewhere in the universe of the spontaneous [...]
CDD Vault Update: Importing Data: Faster and Easier Mapping July 29, 2011 - Importing Data: Faster and Easier Mapping We’ve further refined the mapper to make it quicker and more intuitive. Here’s the new design: In addition to the design refresh, we have streamlined the data import process to only three steps. There’s now a link to create a mapping template on step two, in addition to the [...]
Christopher Lipinski – Drug Repositioning Panel Talk Transcript July 20, 2011 - Christopher Lipinski Okay. Well I’m very glad to be able to participate in this webinar and what I’m going to do is I’m going to talk about sort of science issues in drug repositioning, and I’m going to really put it in the context of the problems that we have nowadays in drug discovery, [...]
David Cavalla – Drug Repositioning Panel Talk Transcript July 20, 2011 - David Cavalla So I’ve just got a few slides here, hoping to pick out a couple of points on Drug Repurposing. The title emphasizes two points, obviously looking ahead but also trying to make use of a retrospective view. So what I’m trying to convey in that title is the idea of seeing a little [...]
Noel Southall – Drug Repositioning Panel Discussion Transcript July 20, 2011 - Noel Southall So actually in the interest of time, I might actually skip my slide overview and actually turn this more back into a panel discussion just by referencing some of the points from the previous talks. I think Chris really gave an excellent presentation that raised some really interesting points. But first to go [...]
Dr. Ellen Berg, Asterand July 19, 2011 - "I was always interested in sort of the bench-to-bedside areas; how do we do a better job of finding new drugs that are actually going to work in people safely."
Thalidomide: Poster Child for Drug Repurposing July 7, 2011 - To whet the appetite for next week’s Drug Repositioning Conference & CDD Chaired panel on broadcast live via GoToWebinar w/ Drs. Christopher Lipinski, David Cavalla, and Noel Southall, we are sharing thoughts on Thalidomide – the “poster child for drug repurposing”. Thalidomide, infamous for producing so called “thalidomide babies” in the 1950’s when used for [...]
The Cause of ADHD…or the Key to Accelerating Human Enlightenment? July 6, 2011 - Is the variant of the dopamine-processing gene DRD4 the cause of ADHD (Attention Deficit Hyperactivity Disorder), the key to accelerating human enlightenment – or both? At CDD, we are honored to support researchers’ collective quests to discover new drug candidates. In fields as broad as chemistry interacting with biology, better mining and collaborative tools [...]
Supreme Court 5-4 and 6-3 Victories for the Drug Discovery Business June 25, 2011 - Two rulings by the Supreme Court earlier this week provide some positive news for the drug discovery business. The first ruling minimizes patient litigation against makers of generic drugs. Generic drug makers use the same warning label as the initial company that discovered the drug. The court basically says it trusts the FDA’s judgement [...]
“If you miss the train I’m on…” June 22, 2011 - …why am I channeling train songs by Peter Paul and Mary this morning? Because today is the 3rd excellent TRAIN series I’ve attended as part of a new program by Faster Cures. I think this type of series points to how information will be effectively shared in our industry in the future. Today it [...]
CDD Vault Update: Dose-Response Improvements Part II: IC50s, MICs and More, Oh My! June 3, 2011 - Easier Import Dose-response data is now imported in a two-column format (e.g. concentration and activity) which means you no longer have to pre-define your dose series. This allows for variable concentrations across samples and enables you to import data directly from screening plates. We have deleted all mapping templates for dose-response data, because they no [...]
Jim Wikel, Ex-Eli Lilly, Apex Therapeutics May 19, 2011 - "I came from southern West Virginia, the coal fields of southern West Virginia, and it wasn’t that common for folks to go to college...when I retired, I was head of Computational Chemistry and Structural Biology with Lilly."
CDD Vault Update: Dose-Response Improvements Part I: Consistency! May 12, 2011 - The calculation of dose-response data is now consistent throughout CDD. Previously we would calculate one EC50 for each row of data, but on the plot we would aggregate all the data by batch/run and perform a separate calculation. Now, all dose-response calculations are performed using the aggregate data from each batch/run, so the numbers in [...]
FDA Panel Unanimously Approves Two New Hep C drugs April 30, 2011 - Amid all the angst regarding the high costs of drug discovery, it is refreshing to see two new drugs for Hepatitis C approved by FDA advisory panels. In the past two days the Antiviral Drugs Advisory Committee of the U.S. Food and Drug Administration (FDA) unanimously approved Merck’s investigational medicine VICTRELIS™ (boceprevir) and Vertex’s [...]
NCATS April 28, 2011 - It is not every day that the NIH creates a new center, but the proposed National Center for Advancing Translational Sciences (NCATS) is just that. There is an interesting dialog separating the NCATS fiction from fact here.
CDD Resources for World Malaria Day (25 April 2011) April 25, 2011 - Today (25 April) is World Malaria Day. In addition to doing our little part hosting Public Malaria Drug Discovery Data (ranging from the discovery of early anti-Malarial compounds during WWII to GSK’s recent release of enzyme and cell screening data) and supporting researchers’ pre-publication data in private CDD Vaults – here are two sites with [...]
CDD Wins Prestigious BioIT 2011 Best Practices Editors’ Choice Award April 14, 2011 - 
We are pleased to announce today that we have just been awarded the BioIT Editors' Choice Best Practice Award for our work supporting tuberculosis researchers at NIAID and the TB Alliance. This award acknowledges two years of software development and support for TB research groups funded by the BMGF, and is a credit to all CDD users and community members who have helped guide our technology over the past seven years in the cloud.
Dr. James McKerrow, UCSF March 29, 2011 - As CDD’s first major customer, Dr. McKerrow guided us in our early days and introduced us to the Gates Foundation, making him perfect for our first CDD Spotlight.
CDD Vault Update: Use Your Own Lingo March 4, 2011 - Would you rather say “assay” than “protocol”? Does “experiment” make more sense to you than “run”? We now allow the administrators of each Vault to choose their own synonyms for the following terms: molecule, batch, protocol, run,readout definition and readout. The place to set these is under the Settings sub-tab in the Manage Vault section. So track down your Vault admin [...]
CDD Vault Update: Data Upload Improvements February 14, 2011 - Importing your data is a critical and often tricky first step when using CDD. This is the first in a series of releases aimed at making data upload faster and easier. Look for the following: Create a run on-the-fly! Yes, you read correctly, you can now create a run on step 2 of the Import [...]
CDD Vault Update: And… the Portal is gone! February 8, 2011 - The sidebar now allows you to control exactly which data (public and private) you want to see, all from a single interface: no more tiers, different versions of pages, or disappearing edit links. We’ve moved all searches you saved at the portal level into your Vault to provide a seamless transition. If you’re still using [...]
CDD co-authors TB molecular mimics paper and review on computational databases, pathway and cheminformatics tools for TB drug discovery February 7, 2011 - The estimate that more lives may have been lost in 2009 due to tuberculosis (TB) than in any year in history is alarming. Approximately 9.2 million new cases and 1.8 million deaths due to TB were reported in 2008. The widespread prevalence of Mycobacterium tuberculosis strains that are resistant to drugs currently used to treat [...]
CDD Vault Update: Show/Hide Projects and Data Sets January 5, 2011 - Back from the holiday break and ready to rock. We continue to focus our efforts on projects, but have decided to make some small tweaks to existing features along the way. Show/Hide projects and data sets Inundated with projects from way back when? Keep active projects in the sidebar and hide the rest. Use the [...]
CDD Vault Update: Saved Searches and Messages for Projects December 17, 2010 - A few more tweaks before enjoying the holidays. Based on feedback and potential IP concerns, saved searches are now project specific at the vault level. Click the “save this search” link on the search page, type in a name and select a project. When posting a message, the list of people you can notify is now updated [...]
CDD Vault Update: Move a Run Between Projects December 10, 2010 - We have been busy enhancing the initial project-related capabilities released on November 19th. Based on your feedback, we also added the following new features: Move a run You can now move a run from one project to another. After clicking on a specific run date, click the Run Details subtab. On the side, click the “Move [...]
CDD Featured in Bio-IT World November 30, 2010 - CDD was recently featured in the article “Changing the Game of Collaborative Drug Discovery” in the Bio-IT World magazine. Kevin Davies of Bio-IT World showcases CDD’s efforts to bring down the walls within the drug discovery ecosystem using the cloud, as well as our work with the Gates Foundation and Tuberculosis. Read the full text here!
CDD Featured on the Cover of MedChemComm November 26, 2010 - Dr. Sean Ekins of CDD, along with Dr. Antony Williams of ChemSpider recently published a paper entitled “Meta-analysis of molecular property patterns and filtering of public datasets of antimalarial “hits” and drugs” in Issue 5 of MedChemComm. The article is featured on the front page of the issue. Read the article here, and take a [...]
CDD Vault Update: Manage Projects Page November 25, 2010 - We performed some minor cleanup tasks and added help messages to the Manage Projects page and the search results. You can again see public data set descriptions by clicking on the “More…” link in the sidebar.
CDD Vault Update: Project-Based Collaboration November 19, 2010 - … and we’re back! We’ve spent the last three months building projects, the next generation of CDD Collaborate. Introduction We built projects to help you do the following kinds of things: Collaborate on live data: Colleagues at another institution will be running followup studies on your hit list, and you’d like them to upload the [...]
New White Paper: “Collaborative Drug Discovery: The Rising Importance of Rare And Neglected Diseases” November 19, 2010 - Dr. Sean Ekins has written a new white paper that merges a summary of our recent publications and some of the topics discussed at the recent CDD community meeting on rare and neglected diseases. You can read the white paper here. We hope it raises even more interest in the work done in the rare and neglected disease community [...]
4th Annual CDD Community Meeting for Catalyzing Drug Discovery Research! September 30, 2010 - The 4th Annual CDD Community Meeting, is a 1-day event on October 21st. The CDD Community Meeting is the best place for the CDD community and all scientists to get together, discuss their research projects, and showcase their work to others in the community. Confirmed Speakers: G. Steven Burrill, CEO, Burrill & Company: Life Sciences [...]
CDD Vault Update: Automatically Calculate Average Values June 30, 2010 - With this release, you can now automatically calculate average values for all data you import into CDD. This is helpful if you perform replicate measurements but typically only want to search and view the average of these replicates. We have also significantly expanded outliers functionality to allow you to flag any readout as an outlier, [...]
GSK and Online Communities Create Unique Alliance to Stimulate Open Source Drug Discovery for Malaria May 20, 2010 - GSK becomes first company to freely share chemical structures on 13,500 molecules from its compound library Alliances formed with leading scientific research communities from private industry and public-domain data provider BURLINGAME, Calif. May 19, 2010 — GlaxoSmithKline (GSK) had teamed up with leading public-domain data providers European Bioinformatics Institute (EMBL-EBI), the U.S. National Library of Medicine [...]
CDD Vault Update: Structure Masking and Biologist User Roles May 19, 2010 - In a common scenario encountered by our users, chemical libraries for a project have already been imported, and the individuals who are screening compounds do not want to accidentally add or modify molecules. In another related scenario, some of our users want to allow access to their vaults without disclosing any chemical structures. This release [...]
Accelrys-Symyx Merger: We Welcome the Churn! April 27, 2010 - The recent merger between two of the largest players in the narrow preclinical drug discovery informatics space (Symyx and Accelrys) makes it timely to comment on merger and post merger opportunities and impacts: The cost of developing and supporting traditional technologies (especially outside of the cloud where they must be deployed, updated, supported- and [...]
Congratulations to ChemSpider! April 22, 2010 - Today, Bio-IT World announced the winners of the sixth Best Practices Awards program. We would like to congratulate Tony Williams and the Royal Society of Chemistry for winning the competition’s first Community Service Prize recognizing excellence in open source, which was awarded for ChemSpider. We are proud to provide links from CDD to ChemSpider for [...]
Guest Blog: Dr. Jonathan Baell, Medicinal Chemistry Group Leader, CRC for Cancer Therapeutics at WEHI March 8, 2010 - We at CDD wish to bring attention to useful developments to the community. In this case it was a recently published J. Med. Chem paper brought to our attention by our SAB member Christopher Lipinski titled “New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in [...]
Scatter Plots Are Live on CDD! December 18, 2009 - Just in time for the holiday, we are happy to announce the beta release of a much-requested feature addition to CDD Vault: Scatter Plots. Before we delve into details, note that we’ve implemented this feature without requiring the installation of additional plug-ins and in a way that works for all supported browsers (and even some [...]
CDD Vault Update: Export to CSV November 25, 2009 - Export to CSV This release adds the ability to export any search results in the CSV (Comma Separated Values) format. This is the fastest way to export large amounts of data, and the resulting file can be easily opened with Excel. Your export format preference (XLS, CSV or SDF) is remembered by the application. We [...]
CDD Vault Update: Export dose-response plots to Excel November 20, 2009 - This release wraps up a series of releases focused on data import. We have also included a couple highly requested smaller features (the top two below). The next major feature we plan to tackle before the end of the year is scatter plots. Contact support for a preview. Export dose-response plots to Excel We are happy [...]
CDD Vault Update: Hydrate support November 10, 2009 - Hydrate support (Only for vaults using CDD’s “registration system” module) For each batch we now explicitly record the number of hydrates associated with the given salt of the molecule. This primarily affects batch formula weight calculations. During data import and manual registration, in addition to stripping hydrates from core structures, we now record the number of [...]
CDD Vault Update: Add Prefixes, IUPAC Name Support, Neutralization and More October 30, 2009 - This is a minor release providing several useful new features and a few design and bug fixes. Automatically add prefixes to molecule names, plate names, and batch external identifiers In Data Import Step 2, you can now provide prefixes to prepend to, for example, every molecule name in the file. This is very helpful when [...]
3rd Annual CDD – UCSF Community Meeting, Oct 1 September 15, 2009 - CDD will be hosting our 3rd Annual Community Meeting for Catalyzing Humanitarian and Commercial Drug Discovery Research on Oct 1, 2009, at the J. David Gladstone Institutes at the UCSF Mission Bay Campus. For more information, click here.
Thursday’s Network Outage April 13, 2009 - Many of you noticed that CDD was unavailable for much of the day on Thursday, April 9th. We wanted to take a moment to explain in more detail the events that caused this outage, and to alert you to a new resource, http://status.collaborativedrug.com. Those of you who live in the San Francisco bay area might [...]
We Must Stop Tuberculosis At All Costs – Acknowledge the Efforts on TB Day March 20, 2009 - Tuberculosis (TB) has not only scarred lungs, it has scarred memories, families, communities, countries and, ultimately, it has scarred the world. If you are sitting in front of a computer anywhere in the Western World, and were born after World War II it is highly probable that you are scarred too..this time as a result [...]
Join us on Our LinkedIn Group March 16, 2009 - LinkedIn has become one of the primary sites on the web for people to connect, network, recommend each other and, for our needs, host discussions within a Group of interested parties who care about what Collaborative Drug Discovery is all about. Over the next few months we will be holding some interesting discussions inside the [...]
New Release: Customize Mine Results January 24, 2009 - Last evening we released the latest update to CDD, customizable mine results. This release makes it easy to add (or remove) protocols, readouts, molecule synonyms and/or user-defined fields to/from your mine results, allowing you to customize the displayed data to be most relevant. To access this new feature, perform a mine query, then click the [...]
Distributed Drug Discovery January 22, 2009 - In the inaugural issue of Volume 11 of the Journal of Combinatorial Chemistry Anthony Czarnik commented on the concept of Distributed Drug Discovery, D3. This concept was introduced in papers in that issue by Profs William Scott and Martin O’Donnell of the IUPUI (Indiana University-Purdue University Indianapolis). The three papers are: Distributed Drug Discovery, Part [...]
CDD is moving offices December 29, 2008 - CDD is in a stage of growth, and we will be relocating our offices over the holiday period and opening our doors at a new location. Update your contact details with this new address: 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010. Come and visit with us a while and discuss our efforts to build [...]
Collaborative Drug Discovery Walks the Web to ChemSpider December 12, 2008 - We are all about Collaboration…it’s in our name! Since our databases sit on a growing foundation of small molecules and their potential contributions to drug discovery, it is natural that we would want to connect our structure collection to additional information that could be of value to our users. There are many open resources of [...]
Second Annual CDD Community Meeting October 7, 2008 - The 2nd CDD Community Meeting was wildly successful with 176 registrants and 20 Posters. The symposium speakers presented on important research and collaboration around neglected diseases and orphan drugs. The Keynote presentation by J. Leighton Read of Alloy Ventures provided crucial insight into how pre-clinical research affects clinical drug development. The Discussion Panels featured members [...]
First Annual CDD Community Meeting March 5, 2007 - The meeting provided new perspectives on collaborative research, scientific community development and global health, with a focus on infectious diseases of the developing world. We had 114 people register, 10 posters presented and many great speakers. Presentation Videos and Slides (PDF) Developing drugs for neglected parasitic diseases in an academic incubator James McKerrow, PhD, Sandler [...]