Protein–ligand data at scale to support machine learning | Nature Reviews Chemistry

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Authors and Affiliations

1. Structural Genomics Consortium, University of Toronto and University Health Network, Toronto, Ontario, Canada

   Aled M. Edwards, Matthieu Schapira, Santha Santhakumar, Hui Peng, Maxwell R. Morgan, Sofia Melliou, Rachel J. Harding, Levon Halabelian, Benjamin Haibe-Kains, Claudia Gordijo, Madison M. Edwards, Dalia Barsyte-Lovejoy, Cheryl Arrowsmith & Suzanne Ackloo

2. Pfizer Research and Development, Cambridge, MA, USA

   Dafydd R. Owen

3. IBM Accelerated Discovery Research, Yorktown Heights, NY, USA

   Leili Zhang & Wendy D. Cornell

4. Collaborative Drug Discovery (CDD) Baylor College of Medicine One Baylor Plaza, Houston, TX, USA

   Damian W. Young

5. Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

   Timothy M. Willson, James Wellnitz, Alexander Tropsha, David Drewry, Rafael Counago, Peter J. Brown, Frances M. Bashore & Alison D. Axtman

6. Division of Chemical Biology and Medicinal Chemistry UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

   James Wellnitz & Alexander Tropsha

7. National Institutes of Health, Bethesda, MD, USA

   Yanli Wang

8. Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK

   Jarrod Walsh & Emma Rivers

9. Research & Early Development, Novo Nordisk A/S, Måløv, Denmark

   Erik Vernet

10. Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Frankfurt, Germany

    Claudia Tredup, Amelia Tjaden, Susanne Müller-Knapp, Stefan Knapp & Thomas Hanke

11. Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Frankfurt, Germany

    Claudia Tredup, Amelia Tjaden, Susanne Müller-Knapp, Stefan Knapp & Thomas Hanke

12. Structural Genomics Consortium, School of Pharmacy, University College London, London, UK

    Matthew H. Todd, Snezana Djordjevic & Nicola A. Burgess-Brown

13. Discovery Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany

    Sven Thamm, Florian Montel, Uta Lessel & Amaury Fernández-Montalván

14. Structural Genomics Consortium, Department of Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden

    Michael Sundström & Opher Gileadi

15. Machine Learning and Computational Sciences, Pfizer Research and Development, Berlin, Germany

    Andreas Steffen & Djork-Arné Clevert

16. Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA

    Shaun Stauffer & Jesse A. Coker

17. Center for Molecular Biology and Genetic Engineering (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas/SP. Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP, Brazil

    Lucas Rodrigo de Souza & Mario H. Bengtson

18. National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA

    Min Shen

19. Pfizer Research and Development, Machine Learning and Computational Sciences, Berlin, Germany

    Kristof Schütt

20. Protein Science, Structural Biology and Biophysics, Discovery Sciences, Research and Development, AstraZeneca, Gothenburg, Sweden

    Lovisa Holmberg Schiavone

21. Takeda Pharmaceuticals, San Diego, CA, USA

    Kumar Saikatendu

22. Digital Life Sciences, Nuvisan ICB GmbH, Berlin, Germany

    Dušan Petrović

23. Research & Development, Pharmaceuticals, Bayer AG, Monheim, Germany

    John P. O’Donnell

24. Nuvisan Innovation Campus Berlin GmbH, Berlin, Germany

    Anke Mueller-Fahrnow

25. Protein, Structure and Biophysics, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK

    Juan Carlos Mobarec

26. Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institute, Stockholm, Sweden

    Maurice Michel

27. Center for Molecular Medicine, Karolinska Institute and Karolinska Hospital, Stockholm, Sweden

    Maurice Michel

28. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK

    Andrew R. Leach

29. Discovery Research, Boehringer Ingelheim International GmbH, Ingelheim, Germany

    Oliver Krämer

30. Evotec SE, Hamburg, Germany

    Florian Krieger

31. X-Chem Inc., Waltham, MA, USA

    Anthony Keefe, Marie-Aude Guié & Arrash J. Baghaie

32. Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt, Germany

    Aimo Kannt

33. Bristol Myers Squibb, San Diego, CA, USA

    Scott A. Johnson

34. Structural Genomics Consortium Frankfurt, Goethe University Frankfurt, Frankfurt, Germany

    Sandra Häberle

35. Bristol Myers Squibb, Cambridge, MA, USA

    Emily Rose Holzinger

36. Discovery and Development Technologies, Merck KGaA, Darmstadt, Germany

    Ingo V. Hartung

37. Bayer AG, Drug Discovery Sciences, Berlin, Germany

    Judith Günther

38. Sage Bionetworks, Seattle, WA, USA

    Luca Foschini

39. Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden

    Ola Engkvist

40. Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden

    Ola Engkvist

41. OMass Therapeutics Ltd, ARC, Oxford, UK

    Katharina Duerr

42. HitGen Inc., Chengdu, China

    Dengfeng Dou

43. Abcam, Biomedical Campus, Cambridge, UK

    Alejandra Solache Diaz

44. Data Sciences and Quantitative Biology, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge, UK

    Sergio Martinez Cuesta

45. Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA

    Timothy Cernak

46. proCURE Department, Oncobell Program, Catalan Institute of Oncology (ICO) and Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran y Reynals, L’Hospitalet del Llobregat, Barcelona, Spain

    Albert A. Antolin

Consortia

Corresponding authors

Correspondence to Aled M. Edwards or Dafydd R. Owen.

Competing interests

D.-A.C., K.S. and D.R.O. are shareholders in Pfizer Inc. The Cernak Lab’s research has been supported by MilliporeSigma, Johnson & Johnson, Relay Therapeutics, Merck & Co., Inc., SPT Labtech, National Defense Medical Center, Shanghai University of Traditional Chinese Medicine, Ministry of Education Taiwan, and Entos, Inc. T.C. has consulted for the University of Dundee Drug Discovery Unit, Scorpion Therapeutics, Relay Therapeutics, Amgen, Genentech, Janssen, Pfizer, Vertex, MilliporeSigma, the US Food & Drug Administration, Gilead, AbbVie, Corteva, Syngenta, Firmenich, Biogen, Bayer, UCB Biopharma, National Taiwan University, AstraZeneca, Grunenthal, and Iambic Therapeutics (previously known as Entos, Inc.). He holds equity in Scorpion Therapeutics and is a co-founder and equity holder at Iambic Therapeutics. B.H.-K. is a co-Founder of the MAQC (Massive Analysis and Quality Control) Society and part of the Scientific Advisory Board of: Consortium de recherche biopharmaceutique (CQDM), Quebec, Canada, Break Through Cancer, Commonwealth Cancer Consortium, United States, Canadian Institute of Health Research–Institute of Genetics, Canada, Cancer Grand Challenges, United Kingdom, Shriners Children, United States. He is part of the Executive Committee of the Terry Fox Digital Health and Discovery Platform, Canada and in the Board of Directors of AACR International–Canada, The American Association for Cancer Research, United States. D.W.Y. is co-founder and shareowner of Deliver Therapeutics. I.V.H. is part of the Board of Directors of TenAces Biosciences. A.K. serves on the SAB of Cilcare, Sulfateq BV and Heartbeat.bio. J.C.M. may hold stock options in Astrazeneca. A.M.-F. is the Board Chair of SGC and Conscience. She is also a shareholder for Bayer AG and an external consultant for Nuvisan ICB GmbH. N.B.-B. is on the SAB for Oxford Vacmedix and holds shares of Exact Sciences. A.T. is co-founder of Predictive LLC. A.S.D. holds stocks in DANAHER. F.K. is a shareholder in Evotec SE. A.F.-M. possess Bayer AG shares. A.A.A. is a consultant to Darwin Health and has received grant funding from Vivan Therapeutics and AtG Therapeutics. D.P. holds stock in Novartis.

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Nature Reviews Chemistry thanks Brian Shoichet, Brent Stockwell and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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