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Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.
Lawson, Catherine L; Kryshtafovych, Andriy; Pintilie, Grigore D; Burley, Stephen K; Cerný, Jirí; Chen, Vincent B; Emsley, Paul; Gobbi, Alberto; Joachimiak, Andrzej; Noreng, Sigrid; Prisant, Michael G; Read, Randy J; Richardson, Jane S; Rohou, Alexis L; Schneider, Bohdan; Sellers, Benjamin D; Shao, Chenghua; Sourial, Elizabeth; Williams, Chris I; Williams, Christopher J; Yang, Ying; Abbaraju, Venkat; Afonine, Pavel V; Baker, Matthew L; Bond, Paul S; Blundell, Tom L; Burnley, Tom; Campbell, Arthur; Cao, Renzhi; Cheng, Jianlin; Chojnowski, Grzegorz; Cowtan, K D; DiMaio, Frank; Esmaeeli, Reza; Giri, Nabin; Grubmüller, Helmut; Hoh, Soon Wen; Hou, Jie; Hryc, Corey F; Hunte, Carola; Igaev, Maxim; Joseph, Agnel P; Kao, Wei-Chun; Kihara, Daisuke; Kumar, Dilip; Lang, Lijun; Lin, Sean; Maddhuri Venkata Subramaniya, Sai R; Mittal, Sumit; Mondal, Arup.
Affiliation
  • Lawson CL; RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA. cathy.lawson@rutgers.edu.
  • Kryshtafovych A; Genome Center, University of California, Davis, CA, USA.
  • Pintilie GD; Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
  • Burley SK; RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
  • Cerný J; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
  • Chen VB; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.
  • Emsley P; RCSB Protein Data Bank and San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA.
  • Gobbi A; Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic.
  • Joachimiak A; Department of Biochemistry, Duke University, Durham, NC, USA.
  • Noreng S; MRC Laboratory of Molecular Biology, Cambridge, UK.
  • Prisant MG; Discovery Chemistry, Genentech Inc., San Francisco, CA, USA.
  • Read RJ; , Berlin, Germany.
  • Richardson JS; Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA.
  • Rohou AL; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
  • Schneider B; Structural Biology, Genentech Inc., South San Francisco, CA, USA.
  • Sellers BD; Protein Science, Septerna, South San Francisco, CA, USA.
  • Shao C; Department of Biochemistry, Duke University, Durham, NC, USA.
  • Sourial E; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
  • Williams CI; Department of Biochemistry, Duke University, Durham, NC, USA.
  • Williams CJ; Structural Biology, Genentech Inc., South San Francisco, CA, USA.
  • Yang Y; Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic.
  • Abbaraju V; Discovery Chemistry, Genentech Inc., San Francisco, CA, USA.
  • Afonine PV; Computational Chemistry, Vilya, South San Francisco, CA, USA.
  • Baker ML; RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
  • Bond PS; Chemical Computing Group, Montreal, Quebec, Canada.
  • Blundell TL; Chemical Computing Group, Montreal, Quebec, Canada.
  • Burnley T; Department of Biochemistry, Duke University, Durham, NC, USA.
  • Campbell A; Structural Biology, Genentech Inc., South San Francisco, CA, USA.
  • Cao R; RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
  • Cheng J; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Chojnowski G; Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA.
  • Cowtan KD; York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
  • DiMaio F; Department of Biochemistry, University of Cambridge, Cambridge, UK.
  • Esmaeeli R; Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK.
  • Giri N; Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Grubmüller H; Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA.
  • Hoh SW; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.
  • Hou J; European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany.
  • Hryc CF; York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
  • Hunte C; Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA.
  • Igaev M; Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA.
  • Joseph AP; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.
  • Kao WC; Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
  • Kihara D; York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
  • Kumar D; Department of Computer Science, Saint Louis University, St. Louis, MO, USA.
  • Lang L; Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA.
  • Lin S; Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
  • Maddhuri Venkata Subramaniya SR; Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
  • Mittal S; Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK.
  • Mondal A; Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
Nat Methods ; 21(7): 1340-1348, 2024 Jul.
Article in En | MEDLINE | ID: mdl-38918604
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.
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Full text: 1 Database: MEDLINE Main subject: Models, Molecular / Cryoelectron Microscopy Language: En Year: 2024 Type: Article
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Full text: 1 Database: MEDLINE Main subject: Models, Molecular / Cryoelectron Microscopy Language: En Year: 2024 Type: Article