ArticleNature methods2024
Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.
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Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14citing papers in PubMed
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Who cites it
14 citing papers in PubMed.
- Confidence-guided cryo-EM map optimisation with LocScale-2.0.Nature communications · 2026Article
- Developments and challenges in hit progression within fragment-based drug discovery.Nature communications · 2026Review
- Q-score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps.Acta crystallographica. Section D, Structural biology · 2025Article
- InstaMap: instant-NGP for cryo-EM density maps.Acta crystallographica. Section D, Structural biology · 2025Article
- MELD in Action: Harnessing Data to Accelerate Molecular Dynamics.Journal of chemical information and modeling · 2025Review
- High-resolution protein modeling through Cryo-EM and AI: current trends and future perspectives - a review.Frontiers in molecular biosciences · 2025Review
- Navigating structure-based drug discovery with emerging innovations in physics- and knowledge-based approaches.npj drug discovery · 2025Review
- Ligand identification in CryoEM and X-ray maps using deep learning.Bioinformatics (Oxford, England) · 2024Article
- Ligand Identification in CryoEM and X-ray Maps Using Deep Learning.bioRxiv : the preprint server for biology · 2024Article
- Toward learning a foundational representation of cells and genes.Nature methods · 2024Article
- Embedding AI in biology.Nature methods · 2024Article
- De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM.Nature communications · 2024Article
- Single-Cell Sequencing: High-Resolution Analysis of Cellular Heterogeneity in Autoimmune Diseases.Clinical reviews in allergy & immunology · 2024Review
- Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures.Scientific data · 2024Article
Corrections and comments
- Update of
Authors and funding
81 authors.
Catherine L LawsonRCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA. cathy.lawson@rutgers.edu.ORCID http://orcid.org/0000-0002-3261-7035
Andriy KryshtafovychGenome Center, University of California, Davis, CA, USA.ORCID http://orcid.org/0000-0001-5066-7178
Grigore D PintilieDepartments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
Stephen K BurleyRCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
Jiří ČernýInstitute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic.ORCID http://orcid.org/0000-0002-1969-9304
Vincent B ChenDepartment of Biochemistry, Duke University, Durham, NC, USA.ORCID http://orcid.org/0000-0003-2492-979X
Paul EmsleyMRC Laboratory of Molecular Biology, Cambridge, UK.
Alberto GobbiDiscovery Chemistry, Genentech Inc., San Francisco, CA, USA.
Andrzej JoachimiakStructural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA.ORCID http://orcid.org/0000-0003-2535-6209
Sigrid NorengStructural Biology, Genentech Inc., South San Francisco, CA, USA.
Michael G PrisantDepartment of Biochemistry, Duke University, Durham, NC, USA.
Randy J ReadDepartment of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.ORCID http://orcid.org/0000-0001-8273-0047
Jane S RichardsonDepartment of Biochemistry, Duke University, Durham, NC, USA.ORCID http://orcid.org/0000-0002-3311-2944
Alexis L RohouStructural Biology, Genentech Inc., South San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-3343-9621
Bohdan SchneiderInstitute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic.ORCID http://orcid.org/0000-0001-7855-3690
Benjamin D SellersDiscovery Chemistry, Genentech Inc., San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-4194-1240
Chenghua ShaoRCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
Elizabeth SourialChemical Computing Group, Montreal, Quebec, Canada.
Chris I WilliamsChemical Computing Group, Montreal, Quebec, Canada.
Christopher J WilliamsDepartment of Biochemistry, Duke University, Durham, NC, USA.ORCID http://orcid.org/0000-0002-5808-8768
Ying YangStructural Biology, Genentech Inc., South San Francisco, CA, USA.
Venkat AbbarajuRCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
Pavel V AfonineMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Matthew L BakerDepartment of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA.ORCID http://orcid.org/0000-0001-9039-8523
Paul S BondYork Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.ORCID http://orcid.org/0000-0002-8465-4823
Tom L BlundellDepartment of Biochemistry, University of Cambridge, Cambridge, UK.ORCID http://orcid.org/0000-0002-2708-8992
Tom BurnleyScientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK.ORCID http://orcid.org/0000-0001-5307-348X
Arthur CampbellCenter for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Renzhi CaoDepartment of Computer Science, Pacific Lutheran University, Tacoma, WA, USA.ORCID http://orcid.org/0000-0002-8345-343X
Jianlin ChengDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.ORCID http://orcid.org/0000-0003-0305-2853
Grzegorz ChojnowskiEuropean Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany.ORCID http://orcid.org/0000-0002-3796-8352
K D CowtanYork Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.ORCID http://orcid.org/0000-0002-0189-1437
Frank DiMaioDepartment of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-7524-8938
Reza EsmaeeliDepartment of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA.
Nabin GiriDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.ORCID http://orcid.org/0000-0002-0251-3956
Helmut GrubmüllerTheoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.ORCID http://orcid.org/0000-0002-3270-3144
Soon Wen HohYork Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.ORCID http://orcid.org/0000-0003-1039-8000
Jie HouDepartment of Computer Science, Saint Louis University, St. Louis, MO, USA.ORCID http://orcid.org/0000-0002-8584-5154
Corey F HrycDepartment of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA.
Carola HunteInstitute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0002-0826-3986
Maxim IgaevTheoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.ORCID http://orcid.org/0000-0001-8781-1604
Agnel P JosephScientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK.ORCID http://orcid.org/0000-0002-0997-8422
Wei-Chun KaoInstitute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0001-8687-6334
Daisuke KiharaDepartment of Biological Sciences, Purdue University, West Lafayette, IN, USA.ORCID http://orcid.org/0000-0003-4091-6614
Dilip KumarVerna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.ORCID http://orcid.org/0000-0002-2721-678X
Lijun LangDepartment of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA.ORCID http://orcid.org/0000-0001-6076-2187
Sean LinDivision of Computing & Software Systems, University of Washington, Bothell, WA, USA.
Sai R Maddhuri Venkata SubramaniyaDepartment of Computer Science, Purdue University, West Lafayette, IN, USA.ORCID http://orcid.org/0000-0002-1696-7676
Sumit MittalBiodesign Institute, Arizona State University, Tempe, AZ, USA.ORCID http://orcid.org/0000-0002-5360-8947
Arup MondalDepartment of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA.
Nigel W MoriartyMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Andrew MuenksDepartment of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA.
Garib N MurshudovMRC Laboratory of Molecular Biology, Cambridge, UK.
Robert A NichollsMRC Laboratory of Molecular Biology, Cambridge, UK.ORCID http://orcid.org/0000-0002-8577-8617
Mateusz OlekYork Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
Colin M PalmerScientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK.ORCID http://orcid.org/0000-0002-4883-1546
Alberto PerezDepartment of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA.ORCID http://orcid.org/0000-0002-5054-5338
Emmi PohjolainenTheoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
Karunakar R PothulaInstitute of Biological Information Processing (IBI-7, Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany.
Christopher N RowleyDepartment of Chemistry, Carleton University, Ottawa, Ontario, Canada.
Daipayan SarkarDepartment of Biological Sciences, Purdue University, West Lafayette, IN, USA.ORCID http://orcid.org/0000-0002-4167-2108
Luisa U SchäferInstitute of Biological Information Processing (IBI-7, Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany.
Christopher J SchlicksupMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Gunnar F SchröderInstitute of Biological Information Processing (IBI-7, Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany.ORCID http://orcid.org/0000-0003-1803-5431
Mrinal ShekharCenter for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Dong SiDivision of Computing & Software Systems, University of Washington, Bothell, WA, USA.ORCID http://orcid.org/0000-0001-7039-2589
Abhishek SingharoyBiodesign Institute, Arizona State University, Tempe, AZ, USA.ORCID http://orcid.org/0000-0002-9000-2397
Oleg V SobolevMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-0623-3214
Genki TerashiDepartment of Biological Sciences, Purdue University, West Lafayette, IN, USA.ORCID http://orcid.org/0000-0002-5339-909X
Andrea C VaianaTheoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.ORCID http://orcid.org/0000-0002-8865-0651
Sundeep C VedithiDepartment of Biochemistry, University of Cambridge, Cambridge, UK.ORCID http://orcid.org/0000-0003-3474-4705
Jacob VerburgtDepartment of Biological Sciences, Purdue University, West Lafayette, IN, USA.
Xiao WangDepartment of Computer Science, Purdue University, West Lafayette, IN, USA.ORCID http://orcid.org/0000-0003-4435-7098
Rangana WarshamanageMRC Laboratory of Molecular Biology, Cambridge, UK.
Martyn D WinnScientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK.ORCID http://orcid.org/0000-0003-0496-6796
Simone WeyandDepartment of Biochemistry, University of Cambridge, Cambridge, UK.
Keitaro YamashitaMRC Laboratory of Molecular Biology, Cambridge, UK.ORCID http://orcid.org/0000-0002-5442-7582
Minglei ZhaoDepartment of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
Michael F SchmidDivision of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.ORCID http://orcid.org/0000-0003-1077-5750
Helen M BermanDepartment of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
Wah ChiuDepartments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA. wahc@stanford.edu.ORCID http://orcid.org/0000-0002-8910-3078
Funding
PROJECT 5 - DUKE - STRUCTURE VALIDATION AND IMPROVEMENT FOR PROTEINS AND N. ACIDSP01GM063210 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI ADAMS, PAUL DAVID · 2001 to 2021
$33.5MPDB MANAGEMENT BY THE RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICSR01GM133198 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI BURLEY, STEPHEN K · 2019 to 2023
$19.3MPDB Management by the Research Collaboratory for Structural BioinformaticsR01GM157729 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI STEPHEN K BURLEY · 2024 to 2026
$11.6MUnified Data Resource for Large Complexes Determined by Cryo-Electron MicroscopyR01GM079429 · NIGMS · STANFORD UNIVERSITY · PI CHIU, WAH · 2007 to 2021
$11.6MPhenix: providing high quality software to the research community for crystallography and cryo-EMR24GM141254 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI PAUL David ADAMS · 2021 to 2026
$9.2MComputational Tools for Neutron Protein CrystallographyR01GM071939 · NIGMS · UT-BATTELLE, LLC-OAK RIDGE NATIONAL LAB · PI COATES, LEIGHTON · 2004 to 2019
$4.3MIntegrated Prediction of Protein Struture at 1D, 2D and 3D LevelsR01GM093123 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI CHENG, JIANLIN · 2010 to 2023
$3.8MMolProbity Validation & Corrections: for Crystallography, PDB & BiomedicineR01GM073919 · NIGMS · DUKE UNIVERSITY · PI RICHARDSON, DAVID CLAUDE · 2006 to 2018
$3.7MProtein structure determination from low-resolution experimental dataR01GM123089 · NIGMS · UNIVERSITY OF WASHINGTON · PI DIMAIO, FRANK P · 2017 to 2025
$2.6MStructural and Functional Studies of Molecular Machines Involved in Chemical Modifications of MacromoleculesR35GM143052 · NIGMS · UNIVERSITY OF CHICAGO · PI ZHAO, MINGLEI · 2021 to 2025
$2.1MExtending MolProbity Diagnosis & Healing Methods to Empower Better CryoEM & Xray Models at 2.5-4A Resolution, plus Versioned, Redeposited "GEMS" for Important Individual StructuresR35GM131883 · NIGMS · DUKE UNIVERSITY · PI RICHARDSON, DAVID CLAUDE · 2019 to 2022
$1.7MBuilding protein structure models for intermediate resolution cryo-electron microscopy mapsR01GM133840 · NIGMS · PURDUE UNIVERSITY · PI KIHARA, DAISUKE · 2020 to 2023
$1.6MDeutsche Forschungsgemeinschaft (German Research Foundation) CIBSS - EXC-2189 - 390939984Deutsche Forschungsgemeinschaft (German Research Foundation) RTG 2756DST | Science and Engineering Research Board (SERB) CRG/2022/002761National Science Foundation (NSF) CHE-2235785National Science Foundation (NSF) DBI-1832184National Science Foundation (NSF) DGE-1762114National Science Foundation (NSF) IIS2211598NIGMS NIH HHS P01 GM063210NIGMS NIH HHS R01 GM071939NIGMS NIH HHS R01 GM073919NIGMS NIH HHS R01 GM079429NIGMS NIH HHS R01 GM093123NIGMS NIH HHS R01 GM123089NIGMS NIH HHS R01 GM133198NIGMS NIH HHS R01 GM133840NIGMS NIH HHS R01 GM146340NIGMS NIH HHS R01 GM157729NIGMS NIH HHS R24 GM141254NIGMS NIH HHS R35 GM131883NIGMS NIH HHS R35 GM143052RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) BB/S005099/1RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) BB/S007083/1RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) BB/T012935/1RCUK | Medical Research Council (MRC) MC_UP_A025_1012RCUK | Medical Research Council (MRC) MR/V000403/1U.S. Department of Energy (DOE) DE-AC02-05CH11231U.S. Department of Energy (DOE) DE-AC02-06CH11357U.S. Department of Energy (DOE) DESC0019749U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) P01GM063210U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R01GM071939U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R01GM073919U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R01GM079429U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R01GM123089U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R01GM133198U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R01GM133840U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R01GM146340U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R24GM141254U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R35GM131883Wellcome TrustWellcome Trust (Wellcome) 208398/Z/17/ZWellcome Trust (Wellcome) 209407/Z/17/Z
Abstract
The EMDataResource 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: Escherichia coli beta-galactosidase with inhibitor, SARS-CoV-2 virus RNA-dependent RNA polymerase with covalently bound nucleotide analog and SARS-CoV-2 virus ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. The quality of submitted ligand models and surrounding atoms were analyzed by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics and contact scores. A composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.
Indexed as
Cryoelectron MicroscopyModels, Molecularbeta-GalactosidaseCOVID-19Escherichia coliLigandsProtein ConformationReproducibility of ResultsSARS-CoV-2beta-GalactosidaseLigands
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