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Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.
Lawson, Catherine L; Kryshtafovych, Andriy; Adams, Paul D; Afonine, Pavel V; Baker, Matthew L; Barad, Benjamin A; Bond, Paul; Burnley, Tom; Cao, Renzhi; Cheng, Jianlin; Chojnowski, Grzegorz; Cowtan, Kevin; Dill, Ken A; DiMaio, Frank; Farrell, Daniel P; Fraser, James S; Herzik, Mark A; Hoh, Soon Wen; Hou, Jie; Hung, Li-Wei; Igaev, Maxim; Joseph, Agnel P; Kihara, Daisuke; Kumar, Dilip; Mittal, Sumit; Monastyrskyy, Bohdan; Olek, Mateusz; Palmer, Colin M; Patwardhan, Ardan; Perez, Alberto; Pfab, Jonas; Pintilie, Grigore D; Richardson, Jane S; Rosenthal, Peter B; Sarkar, Daipayan; Schäfer, Luisa U; Schmid, Michael F; Schröder, Gunnar F; Shekhar, Mrinal; Si, Dong; Singharoy, Abishek; Terashi, Genki; Terwilliger, Thomas C; Vaiana, Andrea; Wang, Liguo; Wang, Zhe; Wankowicz, Stephanie A; Williams, Christopher J; Winn, Martyn; Wu, Tianqi.
Afiliación
  • Lawson CL; 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.
  • Adams PD; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Afonine PV; Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA.
  • Baker ML; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Barad BA; Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA.
  • Bond P; Department of Integrated Computational Structural Biology, The Scripps Research Institute, La Jolla, CA, USA.
  • Burnley T; York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
  • Cao R; Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK.
  • Cheng J; Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA.
  • Chojnowski G; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.
  • Cowtan K; European Molecular Biology Laboratory, c/o DESY, Hamburg, Germany.
  • Dill KA; York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
  • DiMaio F; Laufer Center, Stony Brook University, Stony Brook, NY, USA.
  • Farrell DP; Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA.
  • Fraser JS; Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA.
  • Herzik MA; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
  • Hoh SW; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
  • Hou J; York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
  • Hung LW; Department of Computer Science, Saint Louis University, St. Louis, MO, USA.
  • Igaev M; Los Alamos National Laboratory, Los Alamos, NM, USA.
  • Joseph AP; Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
  • Kihara D; Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK.
  • Kumar D; Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
  • Mittal S; Department of Computer Science, Purdue University, West Lafayette, IN, USA.
  • Monastyrskyy B; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
  • Olek M; Biodesign Institute, Arizona State University, Tempe, AZ, USA.
  • Palmer CM; School of Advanced Sciences and Languages, VIT Bhopal University, Bhopal, India.
  • Patwardhan A; Genome Center, University of California, Davis, CA, USA.
  • Perez A; York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
  • Pfab J; Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK.
  • Pintilie GD; The European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.
  • Richardson JS; Department of Chemistry, University of Florida, Gainesville, FL, USA.
  • Rosenthal PB; Division of Computing & Software Systems, University of Washington, Bothell, WA, USA.
  • Sarkar D; Department of Bioengineering, Stanford University, Stanford, CA, USA.
  • Schäfer LU; Department of Biochemistry, Duke University, Durham, NC, USA.
  • Schmid MF; Structural Biology of Cells and Viruses Laboratory, Francis Crick Institute, London, UK.
  • Schröder GF; Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
  • Shekhar M; Biodesign Institute, Arizona State University, Tempe, AZ, USA.
  • Si D; Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany.
  • Singharoy A; Division of CryoEM and Biomaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA.
  • Terashi G; Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany.
  • Terwilliger TC; Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
  • Vaiana A; Biodesign Institute, Arizona State University, Tempe, AZ, USA.
  • Wang L; Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Wang Z; Division of Computing & Software Systems, University of Washington, Bothell, WA, USA.
  • Wankowicz SA; Biodesign Institute, Arizona State University, Tempe, AZ, USA.
  • Williams CJ; Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
  • Winn M; New Mexico Consortium, Los Alamos, NM, USA.
  • Wu T; Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
Nat Methods ; 18(2): 156-164, 2021 02.
Article en En | MEDLINE | ID: mdl-33542514
ABSTRACT
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.
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Texto completo: 1 Bases de datos: MEDLINE Asunto principal: Modelos Moleculares / Microscopía por Crioelectrón Tipo de estudio: Prognostic_studies Idioma: En Revista: Nat Methods Asunto de la revista: TECNICAS E PROCEDIMENTOS DE LABORATORIO Año: 2021 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
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Texto completo: 1 Bases de datos: MEDLINE Asunto principal: Modelos Moleculares / Microscopía por Crioelectrón Tipo de estudio: Prognostic_studies Idioma: En Revista: Nat Methods Asunto de la revista: TECNICAS E PROCEDIMENTOS DE LABORATORIO Año: 2021 Tipo del documento: Article País de afiliación: Estados Unidos