ArticleResearch square2024
Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge.
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Article in Research square, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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81 authors at 20 institutions in 7 countries.
Catherine L LawsonInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.ORCID 0000-0002-3261-7035
Andriy KryshtafovychGenome Center, University of California, Davis, CA, USA.ORCID 0000-0001-5066-7178
Grigore D PintilieDepartments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
Stephen K BurleyInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
Jiří ČernýInstitute of Biotechnology, Czech Academy of Sciences, Vestec, CZ.ORCID 0000-0002-1969-9304
Vincent B ChenDepartment of Biochemistry, Duke University, Durham NC, USA.
Paul EmsleyMRC Laboratory of Molecular Biology, Cambridge, UK.
Alberto GobbiDiscovery Chemistry, Genentech Inc, South San Francisco, USA.
Andrzej JoachimiakStructural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA.ORCID 0000-0003-2535-6209
Sigrid NorengStructural Biology, Genentech Inc, South San Francisco, USA.
Michael PrisantDepartment of Biochemistry, Duke University, Durham NC, USA.
Randy J ReadDepartment of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.ORCID 0000-0001-8273-0047
Jane S RichardsonDepartment of Biochemistry, Duke University, Durham NC, USA.ORCID 0000-0002-3311-2944
Alexis L RohouStructural Biology, Genentech Inc, South San Francisco, USA.
Bohdan SchneiderInstitute of Biotechnology, Czech Academy of Sciences, Vestec, CZ.
Benjamin D SellersDiscovery Chemistry, Genentech Inc, South San Francisco, USA.
Chenghua ShaoInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
Elizabeth SourialChemical Computing Group, Montreal, Quebec, CA.
Chris I WilliamsChemical Computing Group, Montreal, Quebec, CA.
Christopher J WilliamsDepartment of Biochemistry, Duke University, Durham NC, USA.ORCID 0000-0002-5808-8768
Ying YangStructural Biology, Genentech Inc, South San Francisco, USA.
Venkat AbbarajuInstitute 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 0000-0001-9039-8523
Paul S BondYork Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.ORCID 0000-0002-8465-4823
Tom L BlundellDepartment of Biochemistry, University of Cambridge, Cambridge, UK.ORCID 0000-0002-2708-8992
Tom BurnleyScientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK.ORCID 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 0000-0002-8345-343X
Jianlin ChengDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.ORCID 0000-0003-0305-2853
Grzegorz ChojnowskiEuropean Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany.ORCID 0000-0002-3796-8352
Kevin D CowtanYork Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.ORCID 0000-0002-0189-1437
Frank DiMaioDepartment of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA.ORCID 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.
Helmut GrubmüllerTheoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.ORCID 0000-0002-3270-3144
Soon Wen HohYork Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.ORCID 0000-0003-1039-8000
Jie HouDepartment of Computer Science, Saint Louis University, St. Louis, MO, USA.ORCID 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, 79104 Freiburg, Germany.ORCID 0000-0002-0826-3986
Maxim IgaevTheoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.ORCID 0000-0001-8781-1604
Agnel P JosephScientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK.ORCID 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, 79104 Freiburg, Germany.
Daisuke KiharaDepartment of Biological Sciences, Purdue University, West Lafayette, IN, USA.ORCID 0000-0003-4091-6614
Dilip KumarVerna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
Lijun LangDepartment of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA.ORCID 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 0000-0002-1696-7676
Sumit MittalBiodesign Institute, Arizona State University, Tempe, AZ, USA.ORCID 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.
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 0000-0002-4883-1546
Alberto PerezDepartment of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA.ORCID 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, ON, Canada.
Daipayan SarkarDepartment of Biological Sciences, Purdue University, West Lafayette, IN, USA.ORCID 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 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 0000-0001-7039-2589
Abhishek SingharoyBiodesign Institute, Arizona State University, Tempe, AZ, USA.ORCID 0000-0002-9000-2397
Oleg V SobolevMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID 0000-0002-0623-3214
Genki TerashiDepartment of Biological Sciences, Purdue University, West Lafayette, IN, USA.ORCID 0000-0002-5339-909X
Andrea C VaianaTheoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
Sundeep C VedithiDepartment of Biochemistry, University of Cambridge, Cambridge, UK.
Jacob VerburgtDepartment of Biological Sciences, Purdue University, West Lafayette, IN, USA.
Xiao WangDepartment of Biological Sciences, Purdue University, West Lafayette, IN, USA.ORCID 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 0000-0003-0496-6796
Simone WeyandDepartment of Biochemistry, University of Cambridge, Cambridge, UK.
Keitaro YamashitaMRC Laboratory of Molecular Biology, Cambridge, UK.ORCID 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 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.ORCID 0000-0002-8910-3078
Duke University · USPurdue University West Lafayette · USRutgers, The State University of New Jersey · USLawrence Berkeley National Laboratory · USUniversity of Cambridge · GBUniversity of Florida · USArizona State University · USForschungszentrum Jülich · DEMax Planck Institute for Multidisciplinary SciencesMRC Laboratory of Molecular Biology · GBScience and Technology Facilities Council · GBStanford University · USUniversity of Washington · USUniversity of York · GBBaylor College of Medicine · USBroad Institute · USUniversity of Chicago · USUniversity of Freiburg · DEUniversity of Missouri · USCarleton University · CA
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
$33.5MUnified 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
$4.3MMolProbity 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
$2.6MExtending 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
$1.6MDeep learning methods for automated and accurate reconstruction of protein structures from cryo-EM image dataR01GM146340 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI CHENG, JIANLIN · 2022 to 2025
$1.4MMedical Research Council MC_UP_A025_1012Medical Research Council MR/V000403/1NIGMS NIH HHS P01 GM063210NIGMS NIH HHS R01 GM071939NIGMS NIH HHS R01 GM073919NIGMS NIH HHS R01 GM079429NIGMS NIH HHS R01 GM123089NIGMS NIH HHS R01 GM133840NIGMS NIH HHS R01 GM146340NIGMS NIH HHS R24 GM141254NIGMS NIH HHS R35 GM131883Wellcome Trust
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:
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.