Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks.
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| Title: | Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. |
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| Authors: | Koehler Leman J; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, 10010, USA. julia.koehler.leman@gmail.com.; Department of Biology, New York University, New York, NY, 10003, USA. julia.koehler.leman@gmail.com., Lyskov S; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA., Lewis SM; Cyrus Biotechnology, 1201 Second Ave, Suite 900, Seattle, WA, 98101, USA., Adolf-Bryfogle J; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, 92037, USA.; IAVI Neutralizing Antibody Center, Scripps Research, La Jolla, CA, 92037, USA., Alford RF; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA., Barlow K; Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA, 94158, USA., Ben-Aharon Z; Department of Microbiology and Molecular Genetics, Hebrew University, Hadassah Medical School, POB 12272, Jerusalem, 91120, Israel., Farrell D; Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.; Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA., Fell J; Genome Center, University of California, Davis, CA, 95616, USA.; Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, 95616, USA.; Department of Chemistry, University of California, Davis, CA, 95616, USA., Hansen WA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA.; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA., Harmalkar A; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA., Jeliazkov J; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA., Kuenze G; Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.; Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA.; Institute for Drug Discovery, Medical School, Leipzig University, 04103, Leipzig, Germany., Krys JD; Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland., Ljubetič A; Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.; Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA., Loshbaugh AL; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.; Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, 94158, USA., Maguire J; Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA., Moretti R; Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.; Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA., Mulligan VK; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, 10010, USA., Nance ML; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA., Nguyen PT; Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, 95616, USA., Ó Conchúir S; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA., Roy Burman SS; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA., Samanta R; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA., Smith ST; Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA.; Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, 37235, USA., Teets F; Department of Bioochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27516, USA., Tiemann JKS; Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200, Copenhagen N., Denmark., Watkins A; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA., Woods H; Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA.; Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, 37235, USA., Yachnin BJ; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA.; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA., Bahl CD; Institute for Protein Innovation, Boston, MA, 02115, USA.; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA.; Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA., Bailey-Kellogg C; Department of Computer Science, Dartmouth, Hanover, NH, 03755, USA., Baker D; Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.; Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA., Das R; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA., DiMaio F; Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.; Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA., Khare SD; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA.; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA., Kortemme T; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.; Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, 94158, USA., Labonte JW; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA., Lindorff-Larsen K; Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200, Copenhagen N., Denmark., Meiler J; Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.; Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA.; Institute for Drug Discovery, Medical School, Leipzig University, 04103, Leipzig, Germany., Schief W; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, 92037, USA.; IAVI Neutralizing Antibody Center, Scripps Research, La Jolla, CA, 92037, USA., Schueler-Furman O; Department of Microbiology and Molecular Genetics, Hebrew University, Hadassah Medical School, POB 12272, Jerusalem, 91120, Israel., Siegel JB; Genome Center, University of California, Davis, CA, 95616, USA.; Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, 95616, USA.; Department of Chemistry, University of California, Davis, CA, 95616, USA., Stein A; Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200, Copenhagen N., Denmark., Yarov-Yarovoy V; Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, 95616, USA., Kuhlman B; Department of Bioochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27516, USA., Leaver-Fay A; Department of Bioochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27516, USA., Gront D; Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland., Gray JJ; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA. jgray@jhu.edu., Bonneau R; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, 10010, USA. bonneau@nyu.edu.; Department of Biology, New York University, New York, NY, 10003, USA. bonneau@nyu.edu.; Department of Computer Science, New York University, New York, NY, 10003, USA. bonneau@nyu.edu. |
| Source: | Nature communications [Nat Commun] 2021 Nov 29; Vol. 12 (1), pp. 6947. Date of Electronic Publication: 2021 Nov 29. |
| Publication Type: | Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S. |
| Journal Info: | Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE |
| Database: | MEDLINE Ultimate |
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| ISSN: | 2041-1723 |
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| DOI: | 10.1038/s41467-021-27222-7 |
