Musings on the World of Drug Discovery

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 the premier collaborative drug discovery software platform on the market!

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 lists of relevant articles with each other, and 2) to provide a convenient way to link back to the original article when curating data from literature. We have addressed the first goal with this release, and are now working on the second goal, which we plan to release soon.

With this release we’ve made it convenient to search PubMed for articles, and to then import the relevant ones into your private CDD database. You can also upload PDFs to share with colleagues in your private group (and only within your private group, which is permitted fair use of these often copyrighted materials).

A few other important fixes were also included in this release:

• (+), (-) and (+-) or (+,-) or (+/-) or (+ -) are now permitted in molecule names: This was a slightly embarrassing issue of overzealous molecule name canonicalization that caused problems for some users. You can rest easy now knowing that the name (+)-epinephrine is considered different from (-)-epinephrine by the CDD database.
• Both ChemAxon Extended SMILES and standard SMILES are now provided in Excel/SD exports. When exporting to Excel/SD file and remapping and slurping structures into CDD, always remember to use the ChemAxon Extended SMILES instead of standard SMILES. Standard SMILES is also provided if needed for other applications. Extended SMILES supports some annotations that standard SMILES does not, but MOL files do. For example, R-group labels in Markush structures, or relative versus absolute stereoconfiguration.
• We now check whether batch dates are valid dates when slurping. These will show up as errors in the QC report, instead of silently causing problems after you accept the report. So, for example, “NA” as a batch date is explicitly no longer accepted.

We hope you find the new functionality useful, and as always we welcome your feedback at support@collaborativedrug.com.

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 datasets. The present list of Public Access datasets can be found here. Keep checking this page. More datasets will be showing up shortly.

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 structure-based content available on the internet. Some of those resources include PubChem, DrugBank, KEGG and many other databases. We want to focus our resources on developing the CDD software platform and partner with those resources providing the greatest value to our users so, when selecting a public  resource for providing additional information we chose ChemSpider.

ChemSpider is a free resource for chemists providing access to over 21 million unique chemical entities sourced from almost 150 data sources, many of these of value to drug discovery scientists. ChemSpider has already indexed PubChem, Wikipedia, DrugBank, PubChem and many other valuable resources. We don’t have to do that work. ChemSpider also actively curates and enhances the data on an ongoing basis using a crowdsourcing approach. We all benefit.

As an example of the linking between records the following integration path is shown below with the ChemSpider link highlighted. When this is selected you are taken directly to the ChemSpider record as shown below, in this case into the ChemSpider record here.

ChemSpider has a series of web services available that we might take further advantage of in the future. For now we are happy to connect across the web to the spider.

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 large oaks analogy and talk about how it applies to Collaborative Drug Discovery. We established our company with the intention of making a real difference in the world. With a focus of helping drug discovery scientists around the world by delivering a software environment to archive, mine and collaborate we believe that we can make a real contribution to the process of discovery. We are proud of what we have been able to deliver using a very small team of committed and passionate individuals but we want to deliver more. In order to do so we are expanding our team, expanding our space and, over the next few months, you will see expand our reach in terms of collaborations and projects. In January 2009 we will be moving from our present offices and are now in the process of expanding our team. We are presently looking for a Community Support Professional and a Senior Software Developer as listed on our Jobs page. We are in an exciting phase of growth yet remain focused on our intention of delivering the premier software platform for collaborative drug discovery. Watch this space…

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 any therapeutic area.

We have found a way to balance providing access to this information to the maximum number of scientists while still having a significant commercial offering to support a long-term sustainable and growing business. To obtain this we have created an access policy that is quite black-and-white. For free read-only “public access”, anyone can self-register online to take advantage of a constantly growing body of public data in a constantly evolving and increasingly popular web application.  Commercial access to combined private and public data—with full read, write, export and collaborative capabilities—is available via our standard software-as-a-service subscription.

To be clear:

1. Free public access includes full online capabilities to the CDD application without export capabilities, without the private data archival, and without the advanced private-to-private collaborative capabilities.
2. Full commercial access, in contrast, includes the ability to securely archive private data, to mine private data together with the growing body of public data, and to collaborate within or between groups. Within secure groups in the commercial application one can export the results from any query to Excel files or SD files. Commercial accounts can assign any of several security levels to each individual user as appropriate for each user’s needs for editing or viewing data.

Furthermore, to fully appreciate the benefits of CDD’s valuable product and services, researchers can obtain a free month’s access to the full commercial capabilities before buying. These policies are meant to maximize value to the research community and to make it a delightful experience for all involved.

Although the technology we’ve built is very powerful (with easy data upload, export, data mining and collaborative capabilities), we’ve placed an equal emphasis on usability and user interface design.  While we believe CDD’s ease of use is second to none, there are always numerous ways to improve, and we welcome input and suggestions. We do not just throw the technology over the fence and hope everything goes well. Kellan Gregory and the Community Interests Group (what would traditionally be called support) pride themselves on superior support services, another reason why adoption of the CDD platform and services has been widespread.

As the community and customer base grows, we want people to appreciate that we are prioritizing thousands of requests from hundreds of customers. Although the core platform is provided as-is, it is constantly improving.  As a service, our agile software development and global data and science teams can prioritize custom work on or outside the CDD application with (perhaps) surprising levels of both quality and speed. We are extraordinarily picky and hire only the best of the best possible staff. We thank the early adopters who believed in us and helped us build out the application and services to the current level; we look forward to even more scientists benefitting from CDD as word spreads.

Where are we going in the future: Upstream towards target validation and downstream towards drug development are the two obvious directions for extension. The CDD platform today is an excellent application to “archive, mine, and collaborate” around any data sets privately, securely with other data sets, and/or openly with public data sets. Even so, there will always be more we can do in our sweet spot of collaborative drug discovery. We are just starting to explore with librarians the ability to extend CDD to entirely different types of heterogeneous data. More immediately, we’ll have more exciting announcements with leading Foundations and Industry partners.  Stay tuned.

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 have seen communication shift in the Web 2.0 era we’ve chosen a blog environment as a way for us to communicate with the community.

ChemSpiderman has already discussed the pros and cons of blogging from his experience. We’re hoping for all the upsides of blogging …sharing our thoughts, gathering your feedback and initiating community discussions. While most blogs tend to represent an individual ours is going to host a number of contributors over the coming months. You’ll meet members of our development team, some of our collaborators and some guest bloggers to discuss and mediate “topics of interest”. We’re looking forward to engaging you, our readers..we’ll see where we go from here….