Alex Clark has been building cheminformatics and computational drug discovery software products since the early 2000's, after spending a decade learning to be a scientist the hard way: running reactions at the lab bench.
Since switching to informatics full time, he has worked on most areas of contemporary chemistry software, whether it be 2D or 3D, large scale (cheminformatics) or small scale (quantum chemistry), big molecules (proteins) or small molecules (drugs). He has a persistent interest in the interface between scientists and software, which continues to challenge our industry, and has done much work on visualization techniques, electronic lab notebooks, and reimagining traditional software for new platforms like mobile, cloud and web.
He publishes regularly in the scientific literature, and has maintained a large number of collaborations since becoming an entrepreneur in 2010. Whenever he is not working on projects for CDD, he continues to maintain his own company, Molecular Materials Informatics, relentlessly experimenting with all manner of future-oriented chemistry software ideas, methods and products. Alex completed his doctorate at the University of Auckland, New Zealand, in 1999, and subsequently relocated to North America.
Education & Training
University of Auckland
B.Sc.: Chemistry, Computer Science
M.Sc.: Inorganic/Organometallic Chemistry (Advisors: L. James Wright & Warren Roper)
Ph.D.: Organometallic Chemistry (Advisors: L. James Wright & Warren Roper)
University of California, Riverside
PostDoctoral Fellow: Fullerene Chemistry (Advisor: Christopher Reed)
IntelliChem Inc., Oregon, USA (now Biovia)
Computational Scientist
Chemical Computing Group Inc., Montréal, Canada
Research Scientist
Memberships
Research Interests
Citations
| Citations | 2015 | 1259 |
| h-index | 27 | 20 |
| i10-index | 40 | 32 |
Publications
| PUBLICATION TITLE | CITED BY | PUB YEAR |
|---|---|---|
| Using machine learning to parse chemical mixture descriptions
A.M. Clark, P. Gedeck, P.P. Cheung, B.A. Bunin, ACS Omega, 6, 22400-22409 |
2021 | |
| Capturing mixture composition: an open machine-readable format for representing mixed substances
A.M. Clark, L.R. McEwen, P. Gedeck, B.A. Bunin, Journal of Cheminformatics, 11:33 |
8 | 2019 |
| Multiple Machine Learning Comparisons of HIV Cell-Based and Reverse Transcriptase Datasets
K.M. Zorn, T. Lane, D.P. Russo, A.M. Clark, V. Makarov, S. Ekins, Molecular Pharmaceutics, 11, 696-706 |
39 | 2019 |
| Ebola Virus Bayesian Machine Learning Models Enable New in Vitro Leads
M. Anantpadma, K.M. Zorn, M.A. Lingerfelt, A.M. Clark, J.S. Freundlich, R.A. Davey, P.B. Madrid, S. Ekins, ACS Omega, 4, 2353-2361 |
36 | 2019 |
| Exploiting machine learning for end-to-end drug discovery and development
S. Ekins, A.C. Puhl, K.M. Zorn, T.R. Lane, D.P. Russo, J.J. Klein, A.J. Hickey, A.M. Clark, Nature Materials, 18, 435-441 |
230 | 2019 |
| Data Mining and Computational Modeling of High-Throughput Screening Datasets
S. Ekins, A.M. Clark, K. Dole, K. Gregory, A.M. Mcnutt, A. Coulon-Spektor, C. Weatherall, N.K. Litterman, B.A. Bunin, Reporter Gene Assays, 197-221 |
8 | 2018 |
| Comparing and Validating Machine Learning Models for Mycobacterium tuberculosis Drug Discovery
T. Lane, D.P. Russo, K.M. Zorn, A.M. Clark, A. Korotcov, V. Tkachenko, R.C. Reynolds, A.L. Perryman, J.S. Freundlich, S. Ekins, Molecular Pharmaceutics, 15, 4346-4360 |
69 | 2018 |
| Collaborative drug discovery for More Medicines for Tuberculosis (MM4TB)
S. Ekins, A.C. Spektor, A.M. Clark, K. Dole, B.A. Bunin, Drug Discovery Today, 22, 555-565 |
11 | 2017 |
| Hybrid machine-user learning system and process for identifying, accurately selecting and storing scientific data
A.M. Clark, N.K. Litterman, B.A. Bunin, U.S. Patent No. 9,594,743 |
6 | 2017 |
| Open Source Bayesian Models. 3. Composite Models for Prediction of Binned Responses
A.M. Clark, S. Ekins, K. Dole, Journal of Chemical Information and Modeling, 56, 275-285 |
17 | 2016 |
| BioAssay templates for the semantic web
A.M. Clark; N.K. Litterman, J.E. Kranz; P. Gund; K. Gregory; B.A. Bunin, PeerJ Computer Science, 2, e61 |
9 | 2016 |
| The parallel worlds of public and commercial bioactive chemistry data
C.A. Lipinski, N.K. Litterman, C. Southan, A.J. Williams, A.M. Clark, S. Ekins, Journal of Medicinal Chemistry, 58, 2068–2076 |
31 | 2015 |
| Cheminformatics: Mobile Workflows and Data Sources (Chapter 14)
A.M. Clark, The Future of the History of Chemical Information (ACS Symposium Series 1164), 237-253 |
2 | 2015 |
| Machines first, humans second: on the importance of algorithmic interpretation of open chemistry data
A.M. Clark, A.J. Williams, S. Ekins, Journal of Cheminformatics, 7:9 |
30 | 2015 |
| The Need for a Green Electronic Lab Notebook (Chapter 9)
A.M. Clark, S. Ekins, Green Chemistry Strategies for Drug Discovery (RSC Drug Discovery Series), 185-211 |
1 | 2015 |
| Open Source Bayesian Models: I. Application to ADME/Tox and Drug Discovery Datasets
S. Ekins, A.M. Clark, K. Dole, A. Coulon-Spektor, A. McNutt, G. Grass, J.S. Freundlich, R.C. Reynolds, Journal of Chemical Information and Modeling, 55, 1231-1245 |
99 | 2015 |
| Open Source Bayesian Models: II. Mining a "Big Dataset" to Create and Validate Models with ChEMBL
A.M. Clark, S. Ekins, Journal of Chemical Information and Modeling, 55, 1246-1260 |
78 | 2015 |
| Looking Back to the Future: Predicting in Vivo Efficacy of Small Molecules versus Mycobacterium tuberculosis
S. Ekins, R. Pottorf, R.C. Reynolds, A.J. Williams, A.M. Clark, J.S. Freundlich, Journal of Chemical Information and Modeling, 54, 1070–1082 |
41 | 2014 |
| Bigger data, collaborative tools and the future of predictive drug discovery
S Ekins, AM Clark, SJ Swamidass, N Litterman, AJ Williams, Journal of computer-aided molecular design 28 (10), 997-1008 |
26 | 2014 |
| New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0
A.M. Clark, S. Ekins, M. Sarker, Journal of Cheminformatics, 6:38 |
39 | 2014 |
| Mobile modeling in the molecular sciences
C.M. Grulke, A.M. Clark, A.J. Williams, S. Ekins, C. Morris, M.-R. Goldsmith, McGraw-Hill Yearbook of Science and Technology, 229-233 |
2014 | |
| Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation
A.M. Clark, B.A. Bunin, N.K. Litterman, S.C. Schürer, U. Visser, PeerJ, 524 |
21 | 2014 |
| Putting together the pieces: building a reaction-centric electronic lab notebook for mobile devices.
A. Clark, J. Cheminformatics 6 (S-1), 1 |
1 | 2014 |
| Incorporating Green Chemistry Concepts into Mobile Chemistry Applications and Their Potential Uses
S. Ekins, A.M. Clark, A.J. Williams, ACS Sustainable Chemistry and Engineering, 1, 8-13 |
49 | 2013 |
| Cheminformatics workflows using mobile apps
S. Ekins, A.M. Clark, A.J. Williams, Chem-Bio Informatics Journal, 13, 1-18 |
18 | 2013 |
| Four disruptive strategies for removing drug discovery bottlenecks
S. Ekins, C.L. Waller, M.P. Bradley, A.M. Clark, A.J. Williams, Drug Discovery Today, 18, 265–271 |
38 | 2013 |
| TB Mobile: A Mobile App for Anti-tuberculosis Molecules with Known Targets
S. Ekins, A.M. Clark, M. Sarker, Journal of Cheminformatics, 5:13 |
38 | 2013 |
| Rendering Molecular Sketches for Publication Quality Output
A.M. Clark, Molecular Informatics, 32, 291-301 |
6 | 2013 |
| Redefining Cheminformatics with Intuitive Collaborative Mobile Apps
A.M. Clark, S. Ekins, A.J. Williams, Molecular Informatics, 31, 569-584 |
31 | 2012 |
| Open Drug Discovery Teams: A Chemistry Mobile App for Collaboration
S. Ekins, A.M. Clark, A.J. Williams, Molecular Informatics, 31, 585-597 |
40 | 2012 |
| Redefining Cheminformatics with Intuitive Collaborative Mobile Apps
A.M. Clark, S. Ekins, A.J. Williams, Molecular Informatics, 31, 569-584 |
31 | 2012 |
| Open Drug Discovery Teams: A Chemistry Mobile App for Collaboration
S. Ekins, A.M. Clark, A.J. Williams, Molecular Informatics, 31, 585-597 |
2 | 2012 |
| Mobile apps for chemistry in the world of drug discovery
A.J. Williams, S. Ekins, A.M. Clark, J.J. Jack, R.L. Apodaca, Drug Discovery Today, 16, 928-939 |
59 | 2011 |
| Accurate Specification of Molecular Structures: The Case for Zero-Order Bonds and Explicit Hydrogen Counting
A.M. Clark, Journal of Chemical Information and Modeling, 52, 3149-3157 |
18 | 2011 |
| 2D Depiction of Fragment Hierarchies
A.M. Clark, Journal of Chemical Information and Modeling, 50, 37-46 |
17 | 2010 |
| Basic primitives for molecular diagram sketching
A.M. Clark, Journal of Cheminformatics, 2:8 |
32 | 2010 |
| Detection and Assignment of Common Scaffolds in Project Databases of Lead Molecules
A.M. Clark, P. Labute, Journal of Medicinal Chemistry, 52, 469-483 |
57 | 2009 |
| 2D Depiction of Protein−Ligand Complexes
A.M. Clark, P. Labute, Journal of Chemical Information and Modeling, 47, 1933-1944 |
143 | 2007 |
| Flexible 3D pharmacophores as descriptors of dynamic biological space
J.H. Nettles, J.L. Jenkins, C. Williams, A.M. Clark, A. Bender, Z. Deng, J.W. Davies, M. Glick, Journal of Molecular Graphics and Modelling, 26, 622-633 |
46 | 2007 |
| 2D Structure Depiction
A.M. Clark, P. Labute, M. Santavy, Journal of Chemical Information and Modeling, 46, 1107-1123 |
64 | 2006 |
| Bis(N,N'-dimethylimidazol-2-ylidene)mercury chlorotriiodomercury dimethyl sulfoxide solvate
A.M. Clark, C.E.F. Rickard, A.G. Oliver, L.J. Wright, W.R. Roper, Acta Crystallographica, C56, 26 |
9 | 2000 |
| Bromination and nitration reactions of metallated (Ru and Os) multiaromatic ligands and crystal structures of selected products
A.M. Clark, C.E.F. Rickard, W.R. Roper, L.J. Wright, Journal of Organometallic Chemistry, 598, 262 |
47 | 2000 |
| Stepwise Conversion of an Osmium Trimethylstannyl Complex to a Triiodostannyl Complex and Nucleophilic Substitution Reactions at the Tin-iodine Bonds
A.M. Clark, C.E.F. Rickard, T.J. Woodman, L.J. Wright, W.R. Roper, Organometallics, 19, 1766 |
32 | 2000 |
| The origin of the 'spike' in the EPR spectrum of C60-
P. Paul, R.D. Bolskar, A.M. Clark, C.A. Reed, Chemical Communications, 1229 |
18 | 2000 |
| Cyclometallated complexes of ruthenium and osmium containing the o-C6H4PPh2 ligand
M.A. Bennett, A.M. Clark, M. Contel, C.E.F. Rickard, W.R. Roper, L.J. Wright, Journal of Organometallic Chemistry, 601, 299 |
25 | 2000 |
| Ph.D. Thesis: Aryl Organometallic Compounds of Ruthenium and Osmium
A.M. Clark |
1999 | |
| Electrophilic Aromatic Substitution Reactions at the Phenyl Ring of the Chelated 2-(2'-Pyridyl)phenyl) Ligand Bound to Ruthenium(II) or Osmium(II)
A.M. Clark, C.E.F. Rickard, W.R. Roper, L.J. Wright, Organometallics, 18, 2813 |
93 | 1999 |
| 5-Bromination of an η2-8-Quinolyl Ligand Bound to Osmium(II) and Subsequent Lithiation and Derivatization of This Functionalized Ligand
A.M. Clark, C.E.F. Rickard, W.R. Roper, L.J. Wright: Organometallics, 17, 4535 |
21 | 1998 |
| Chemical Resource Kit, Chemistry in New Zealand, Nov/Dec | 1998 | |
| Osmium complexes containing either chelating or non-chelating 8-quinolyl ligands
A.M. Clark, C.E.F. Rickard, W.R. Roper, L.J. Wright, Journal of Organometallic Chemistry, 545-546, 619 |
1997 | |
| M.Sc. Thesis: Synthetic Approaches to Ruthenium and Osmium Stannyl Complexes
A.M. Clark |
1996 | |
| Osmium nitrosyl complexes with osmium-tin bonds; Crystal structure of Os[Sn(p-tolyl)3](NO)(CO)2(PPh3)
A.M. Clark, C.E.F. Rickard, W.R. Roper, L.J. Wright, Journal of Organometallic Chemistry, 543, 111 |
1996 |
Presentations and Webinars
Presentations
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Royal Society of Chemistry Formulation 4.1 Symposium, November 2021
- Mixtures: informatics for formulations and consumer products (Video Recording)
- Mixtures: informatics for formulations and consumer products (Slidedeck
Cambridge Cheminformatics Network Meeting, February 2021
- Mixtures InChI (MInChI): an open machine-readable format for representing mixed substances (Video Recording)
- Mixtures InChI (MInChI): an open machine-readable format for representing mixed substances (Slidedeck)
InChI Virtual Workshop, hosted by NIH (National Institutes of Health), March 2021
- Mixtures InChI: A Story of How Standards Drive Upstream Products (presentation start time, 2:19:36)
- Mixtures InChI: A Story of How Standards Drive Upstream Products (Slidedeck).
CDD Webinars
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