Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge.

Autor:	Lawson CL; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA., 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; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ USA.; San Diego Supercomputer Center, University of California San Diego, La Jolla, CA USA., Černý J; Institute of Biotechnology, Czech Academy of Sciences, Vestec, CZ., Chen VB; Department of Biochemistry, Duke University, Durham NC, USA., Emsley P; MRC Laboratory of Molecular Biology, Cambridge, UK., Gobbi A; Discovery Chemistry, Genentech Inc, South San Francisco, USA., Joachimiak A; Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA., Noreng S; Structural Biology, Genentech Inc, South San Francisco, USA., Prisant M; Department of Biochemistry, Duke University, Durham NC, USA., Read RJ; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK., Richardson JS; Department of Biochemistry, Duke University, Durham NC, USA., Rohou AL; Structural Biology, Genentech Inc, South San Francisco, USA., Schneider B; Institute of Biotechnology, Czech Academy of Sciences, Vestec, CZ., Sellers BD; Discovery Chemistry, Genentech Inc, South San Francisco, USA., Shao C; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA., Sourial E; Chemical Computing Group, Montreal, Quebec, CA., Williams CI; Chemical Computing Group, Montreal, Quebec, CA., Williams CJ; Department of Biochemistry, Duke University, Durham NC, USA., Yang Y; Structural Biology, Genentech Inc, South San Francisco, USA., Abbaraju V; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA., Afonine PV; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Baker ML; Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA., Bond PS; York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK., Blundell TL; Department of Biochemistry, University of Cambridge, Cambridge, UK., Burnley T; Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK., Campbell A; Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Cao R; Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA., Cheng J; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA., Chojnowski G; European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany., Cowtan KD; York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK., DiMaio F; Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA., Esmaeeli R; Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA., Giri N; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA., Grubmüller H; Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany., Hoh SW; York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK., Hou J; Department of Computer Science, Saint Louis University, St. Louis, MO, USA., Hryc CF; Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA., Hunte C; Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany., Igaev M; Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany., Joseph AP; Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK., Kao WC; Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany., Kihara D; Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.; Department of Computer Science, Purdue University, West Lafayette, IN, USA., Kumar D; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA., Lang L; Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA., Lin S; Division of Computing & Software Systems, University of Washington, Bothell, WA, USA., Maddhuri Venkata Subramaniya SR; Department of Computer Science, Purdue University, West Lafayette, IN, USA., Mittal S; Biodesign Institute, Arizona State University, Tempe, AZ, USA.; School of Advanced Sciences and Languages, VIT Bhopal University, Bhopal, India., Mondal A; Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA., Moriarty NW; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Muenks A; Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA., Murshudov GN; MRC Laboratory of Molecular Biology, Cambridge, UK., Nicholls RA; MRC Laboratory of Molecular Biology, Cambridge, UK., Olek M; York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.; Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK., Palmer CM; Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK., Perez A; Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA., Pohjolainen E; Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany., Pothula KR; Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany., Rowley CN; Department of Chemistry, Carleton University, Ottawa, ON, Canada., Sarkar D; Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.; Biodesign Institute, Arizona State University, Tempe, AZ, USA., Schäfer LU; Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany., Schlicksup CJ; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Schröder GF; Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany.; Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany., Shekhar M; Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Biodesign Institute, Arizona State University, Tempe, AZ, USA., Si D; Division of Computing & Software Systems, University of Washington, Bothell, WA, USA., Singharoy A; Biodesign Institute, Arizona State University, Tempe, AZ, USA., Sobolev OV; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Terashi G; Department of Biological Sciences, Purdue University, West Lafayette, IN, USA., Vaiana AC; Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.; Nature's Toolbox (NTx), Rio Rancho, NM, USA., Vedithi SC; Department of Biochemistry, University of Cambridge, Cambridge, UK., Verburgt J; Department of Biological Sciences, Purdue University, West Lafayette, IN, USA., Wang X; Department of Biological Sciences, Purdue University, West Lafayette, IN, USA., Warshamanage R; MRC Laboratory of Molecular Biology, Cambridge, UK., Winn MD; Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK., Weyand S; Department of Biochemistry, University of Cambridge, Cambridge, UK., Yamashita K; MRC Laboratory of Molecular Biology, Cambridge, UK., Zhao M; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA., Schmid MF; Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA., Berman HM; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA., Chiu W; Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA.; Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
Jazyk:	angličtina
Zdroj:	Research square [Res Sq] 2024 Jan 25. Date of Electronic Publication: 2024 Jan 25.
DOI:	10.21203/rs.3.rs-3864137/v1
Abstrakt:	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: E. coli beta-galactosidase with inhibitor, SARS-CoV-2 RNA-dependent RNA polymerase with covalently bound nucleotide analog, and SARS-CoV-2 ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. We found that (1) the quality of submitted ligand models and surrounding atoms varied, as judged by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics, and contact scores, and (2) 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. Competing Interests: Competing Interests S. Noreng, A. Gobbi, A. Rohou, B. Sellers and Y. Yang are current or former employees of Genentech. The remaining authors declare no competing interests. Additional Declarations: Yes there is potential Competing Interest. S. Noreng, A. Gobbi, A. Rohou, B. Sellers and Y. Yang are current or former employees of Genentech. The remaining authors declare no competing interests.
Databáze:	MEDLINE
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