Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge
- Rutgers Univ., Piscataway, NJ (United States)
- Univ. of California, Davis, CA (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- The University of Texas Health Science Center at Houston, TX (United States)
- The Scripps Research Inst., La Jolla, CA (United States)
- Univ. of York (United Kingdom)
- UKRI Science and Technology Facilities Council, Didcot (United Kingdom)
- Pacific Lutheran University, Tacoma, WA (United States)
- Univ. of Missouri, Columbia, MO (United States)
- Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). European Molecular Biology Laboratory
- Stony Brook Univ., NY (United States)
- Univ. of Washington, Seattle, WA (United States)
- Univ. of California, San Francisco, CA (United States)
- Univ. of California, San Diego, CA (United States)
- Saint Louis University, MO (United States)
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Max Planck Institute for Biophysical Chemistry, Göttingen (Germany)
- Purdue Univ., West Lafayette, IN (United States)
- Baylor College of Medicine, Houston, TX (United States)
- Arizona State Univ., Tempe, AZ (United States); VIT Bhopal University (India)
- The European Bioinformatics Institute (EMBL-EBI), Hinxton (United States)
- Univ. of Florida, Gainesville, FL (United States)
- Univ. of Washington, Bothell, WA (United States)
- Stanford Univ., CA (United States)
- Duke Univ., Durham, NC (United States)
- Francis Crick Institute, London (United Kingdom)
- Purdue Univ., West Lafayette, IN (United States); Arizona State Univ., Tempe, AZ (United States)
- Forschungszentrum Juelich (Germany)
- SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL); Stanford Univ., CA (United States)
- Forschungszentrum Juelich (Germany); Heinrich Heine University Düsseldorf (Germany)
- Arizona State Univ., Tempe, AZ (United States); Broad Institute of MIT and Harvard, Cambridge, MA (United States)
- Arizona State Univ., Tempe, AZ (United States)
- New Mexico Consortium, Los Alamos, NM (United States)
- Janssen Research and Development, Spring House, PA (United States)
- Rutgers Univ., Piscataway, NJ (United States); Univ. of Southern California, Los Angeles, CA (United States)
- Stanford Univ., CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)
This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.
- Research Organization:
- SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Organization:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH); National Institute of General Medical Sciences (NIGMS); National Science Foundation (NSF); Purdue Institute of Drug Discovery; Max Planck Society German Research Foundation; Welch Foundation; Medical Research Council; Wellcome Trust; Biotechnology and Biological Sciences Research Council
- Grant/Contract Number:
- AC02-76SF00515; R01GM079429; AC05-00OR22725; R35GM131883; P01GM063210; MCB-1942763 (CAREER); R01GM095583; R01GM123055; R01GM133840; DMS1614777; CMMI1825941; MCB1925643; DBI2003635; R01GM123159; IG 109/1-1; FOR-1805; R37AI36040; Q1279; DBI2030381; MR/N009614/1; 208398/Z/17/Z; BB/P000517/1; BB/P000975/1; 89233218CNA000001
- OSTI ID:
- 1777461
- Alternate ID(s):
- OSTI ID: 1784701
- Report Number(s):
- LA-UR-20-25444; TRN: US2209463
- Journal Information:
- Nature Methods, Vol. 18, Issue 2; ISSN 1548-7091
- Publisher:
- Nature Publishing GroupCopyright Statement
- Country of Publication:
- United States
- Language:
- English
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