Published February 1, 2024 | Version v1
Dataset Open

2021 EMDataResource Ligand Model Challenge Dataset


  • 1. ROR icon Rutgers, The State University of New Jersey
  • 2. ROR icon University of California, Davis
  • 3. ROR icon Stanford University
  • 4. ROR icon Czech Academy of Sciences
  • 5. ROR icon Duke University
  • 6. ROR icon MRC Laboratory of Molecular Biology
  • 7. ROR icon Genentech
  • 8. ROR icon Argonne National Laboratory
  • 9. ROR icon University of Cambridge
  • 10. Chemical Computing Group
  • 11. ROR icon Lawrence Berkeley National Laboratory
  • 12. ROR icon The University of Texas Health Science Center
  • 13. ROR icon University of York
  • 14. ROR icon Science and Technology Facilities Council
  • 15. ROR icon Broad Institute
  • 16. ROR icon Pacific Lutheran University
  • 17. ROR icon University of Missouri
  • 18. ROR icon European Molecular Biology Laboratory
  • 19. ROR icon University of Washington
  • 20. ROR icon University of Florida
  • 21. ROR icon Max Planck Institute for Multidisciplinary Sciences
  • 22. ROR icon Saint Louis University
  • 23. ROR icon University of Freiburg
  • 24. ROR icon Purdue University West Lafayette
  • 25. ROR icon Baylor College of Medicine
  • 26. ROR icon University of Washington Bothell
  • 27. ROR icon Arizona State University
  • 28. ROR icon Vellore Institute of Technology University
  • 29. ROR icon Diamond Light Source
  • 30. ROR icon Forschungszentrum Jülich
  • 31. ROR icon Carleton University
  • 32. ROR icon Heinrich Heine University Düsseldorf
  • 33. ROR icon University of Chicago


This is the full dataset of the 2021 Cryo-EM Map-based Model Ligand Challenge sponsored by EMDataResource (,, The Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein/nucleic-acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: (1) E. coli beta-galactosidase with inhibitor, (2) SARS-CoV-2 RNA-dependent RNA polymerase with covalently bound nucleotide analog, and (3) SARS-CoV-2 ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details.

File Descriptions:

  • 2021-EMDataResource-Ligand-Challenge-web.pdf: Archive of challenges website content describing the challenge including News, Overview, Goals, Model Evaluation, Timeline, Targets, How to Participate, Q&A, Advisory Committee, Ligand Images
  • Submitted model files for each target (mmCIF and PDB formats) used for analyses
  • S1_Ligand_Challenge_Statistics_Submission_Form.pdf: Overall model statistics, model submission form guide
  • S2_submission_metadata.xlsx: Complete set of metadata collected for each submitted model
  • S3_ligandchallengescores.xlsx: Compiled set of scores for this challenge from the model-compare site.
  • WrapUp_MeetingAgendaLigandChallenge.pdf: Agenda of the July 26-28 2021 wrap up meeting
  • zoom_discussion_mc_results.mp4: July 14 Model-Compare site analysis live demo recording



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Is documented by
Preprint: 10.21203/ (DOI)