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    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

    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 

    (Links open in new tab)

    Royal Society of Chemistry Formulation 4.1 Symposium, November 2021

     

    Cambridge Cheminformatics Network Meeting, February 2021

     

    InChI Virtual Workshop, hosted by NIH (National Institutes of Health), March 2021

     

    CDD Webinars

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