Alex Clark, Ph.D. Research Scientist Collaborative Drug Discovery & CDD Vault

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

Molecular Materials Informatics, Inc.
Founder

Memberships

American Chemical Society

Research Interests

Cheminformatics
Drug Discovery
Electronic Lab Notebooks

Citations

	ALL	SINCE 2016
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