Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.

Autor: 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.; 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.; RCSB Protein Data Bank and San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA., Černý J; Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic., 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., San Francisco, CA, USA.; Berlin, Germany., Joachimiak A; Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA.; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA., Noreng S; Structural Biology, Genentech Inc., South San Francisco, CA, USA.; Protein Science, Septerna, South San Francisco, CA, USA., Prisant MG; 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, CA, USA., Schneider B; Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic., Sellers BD; Discovery Chemistry, Genentech Inc., San Francisco, CA, USA.; Computational Chemistry, Vilya, South San Francisco, CA, USA., Shao C; RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA., Sourial E; Chemical Computing Group, Montreal, Quebec, Canada., Williams CI; Chemical Computing Group, Montreal, Quebec, Canada., Williams CJ; Department of Biochemistry, Duke University, Durham, NC, USA., Yang Y; Structural Biology, Genentech Inc., South San Francisco, CA, USA., Abbaraju V; RCSB Protein Data Bank and 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, 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, 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.; Trivedi School of Biosciences, Ashoka University, Sonipat, India., Lang L; Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA.; The Chinese University of Hong Kong, Hong Kong, China., 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.; National Renewable Energy Laboratory (NREL), Golden, CO, 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.; Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, 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, Ontario, Canada., Sarkar D; Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.; Biodesign Institute, Arizona State University, Tempe, AZ, USA.; MSU-DOE Plant Research Laboratory, East Lansing, MI, USA.; School of Molecular Sciences, 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 Computer Science, 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, USA., Chiu W; Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA. wahc@stanford.edu.; Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA. wahc@stanford.edu.

Publikováno v: Nature methods [Nat Methods] 2024 Jul; Vol. 21 (7), pp. 1340-1348. Date of Electronic Publication: 2024 Jun 25.

The bad and the good of trends in model building and refinement for sparse-data regions: pernicious forms of overfitting versus good new tools and predictions.

Autor: Richardson JS; Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA., Williams CJ; Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA., Chen VB; Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA., Prisant MG; Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA., Richardson DC; Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA.

Publikováno v: Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Dec 01; Vol. 79 (Pt 12), pp. 1071-1078. Date of Electronic Publication: 2023 Nov 03.

Improving SARS-CoV-2 structures: Peer review by early coordinate release.

Autor: Croll TI; CIMR, University of Cambridge, Cambridge, United Kingdom., Williams CJ; Department of Biochemistry, Duke University, Durham, North Carolina., Chen VB; Department of Biochemistry, Duke University, Durham, North Carolina., Richardson DC; Department of Biochemistry, Duke University, Durham, North Carolina., Richardson JS; Department of Biochemistry, Duke University, Durham, North Carolina. Electronic address: jane.richardson@duke.edu.

Publikováno v: Biophysical journal [Biophys J] 2021 Mar 16; Vol. 120 (6), pp. 1085-1096. Date of Electronic Publication: 2021 Jan 16.

New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink "waters," and NGL Viewer to recapture online 3D graphics.

Autor: Prisant MG; Department of Biochemistry, Duke University Medical Center, Durham, North Carolina., Williams CJ; Department of Biochemistry, Duke University Medical Center, Durham, North Carolina., Chen VB; Department of Biochemistry, Duke University Medical Center, Durham, North Carolina., Richardson JS; Department of Biochemistry, Duke University Medical Center, Durham, North Carolina., Richardson DC; Department of Biochemistry, Duke University Medical Center, Durham, North Carolina.

Publikováno v: Protein science : a publication of the Protein Society [Protein Sci] 2020 Jan; Vol. 29 (1), pp. 315-329. Date of Electronic Publication: 2019 Dec 10.

Assessment of detailed conformations suggests strategies for improving cryoEM models: Helix at lower resolution, ensembles, pre-refinement fixups, and validation at multi-residue length scale.

Autor: Richardson JS; Department of Biochemistry, Duke University, Durham, NC 27710, USA. Electronic address: jsr@kinemage.biochem.duke.edu., Williams CJ; Department of Biochemistry, Duke University, Durham, NC 27710, USA., Videau LL; Department of Biochemistry, Duke University, Durham, NC 27710, USA., Chen VB; Department of Biochemistry, Duke University, Durham, NC 27710, USA., Richardson DC; Department of Biochemistry, Duke University, Durham, NC 27710, USA.

Publikováno v: Journal of structural biology [J Struct Biol] 2018 Nov; Vol. 204 (2), pp. 301-312. Date of Electronic Publication: 2018 Aug 11.