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Macromolecular modeling and design in Rosetta: recent methods and frameworks.

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Title: Macromolecular modeling and design in Rosetta: recent methods and frameworks.
Authors: Leman JK; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Julia.koehler.leman@nyu.edu.; Department of Biology, New York University, New York, New York, USA. Julia.koehler.leman@nyu.edu., Weitzner BD; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Lyell Immunopharma Inc., Seattle, WA, USA., Lewis SM; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Biochemistry, Duke University, Durham, NC, USA.; Cyrus Biotechnology, Seattle, WA, USA., Adolf-Bryfogle J; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Alam N; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Alford RF; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA., Aprahamian M; Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA., Baker D; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Barlow KA; Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA, USA., Barth P; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA., Basanta B; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Biological Physics Structure and Design PhD Program, University of Washington, Seattle, WA, USA., Bender BJ; Department of Pharmacology, Vanderbilt University, Nashville, TN, USA., Blacklock K; Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA., Bonet J; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Boyken SE; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Lyell Immunopharma Inc., Seattle, WA, USA., Bradley P; Fred Hutchinson Cancer Research Center, Seattle, WA, USA., Bystroff C; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA., Conway P; Department of Biochemistry, University of Washington, Seattle, WA, USA., Cooper S; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Correia BE; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Coventry B; Department of Biochemistry, University of Washington, Seattle, WA, USA., Das R; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA., De Jong RM; DSM Biotechnology Center, Delft, the Netherlands., DiMaio F; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Dsilva L; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Dunbrack R; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA., Ford AS; Department of Biochemistry, University of Washington, Seattle, WA, USA., Frenz B; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA., Fu DY; Department of Chemistry, Vanderbilt University, Nashville, TN, USA., Geniesse C; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA., Goldschmidt L; Department of Biochemistry, University of Washington, Seattle, WA, USA., Gowthaman R; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA., Gray JJ; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA., Gront D; Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland., Guffy S; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Horowitz S; Department of Chemistry & Biochemistry, University of Denver, Denver, CO, USA.; The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA., Huang PS; Department of Biochemistry, University of Washington, Seattle, WA, USA., Huber T; Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia., Jacobs TM; Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Jeliazkov JR; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA., Johnson DK; Center for Computational Biology, University of Kansas, Lawrence, KS, USA., Kappel K; Biophysics Program, Stanford University, Stanford, CA, USA., Karanicolas J; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA., Khakzad H; Swiss Institute of Bioinformatics, Lausanne, Switzerland.; Institute for Computational Science, University of Zurich, Zurich, Switzerland.; S3IT, University of Zurich, Zurich, Switzerland., Khar KR; Cyrus Biotechnology, Seattle, WA, USA.; Center for Computational Biology, University of Kansas, Lawrence, KS, USA., Khare SD; Institute of 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.; Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, NJ, USA.; Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.; Computational Biology and Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA., Khatib F; Department of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, MA, USA., Khramushin A; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., King IC; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA., Kleffner R; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Koepnick B; Department of Biochemistry, University of Washington, Seattle, WA, USA., Kortemme T; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Kuenze G; Department of Chemistry, Vanderbilt University, Nashville, TN, USA.; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA., Kuhlman B; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Kuroda D; Medical Device Development and Regulation Research Center, School of Engineering, University of Tokyo, Tokyo, Japan.; Department of Bioengineering, School of Engineering, University of Tokyo, Tokyo, Japan., Labonte JW; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.; Department of Chemistry, Franklin & Marshall College, Lancaster, PA, USA., Lai JK; Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA., Lapidoth G; Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel., Leaver-Fay A; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Lindert S; Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA., Linsky T; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., London N; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Lubin JH; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA., Lyskov S; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA., Maguire J; Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Malmström L; Swiss Institute of Bioinformatics, Lausanne, Switzerland.; Institute for Computational Science, University of Zurich, Zurich, Switzerland.; S3IT, University of Zurich, Zurich, Switzerland.; Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden., Marcos E; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain., Marcu O; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Marze NA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA., Meiler J; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.; Departments of Chemistry, Pharmacology and Biomedical Informatics, Vanderbilt University, Nashville, TN, USA.; Institute for Chemical Biology, Vanderbilt University, Nashville, TN, USA., Moretti R; Department of Chemistry, Vanderbilt University, Nashville, TN, USA., Mulligan VK; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Nerli S; Department of Computer Science, University of California Santa Cruz, Santa Cruz, CA, USA., Norn C; Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel., Ó'Conchúir S; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Ollikainen N; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Ovchinnikov S; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA., Pacella MS; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA., Pan X; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Park H; Department of Biochemistry, University of Washington, Seattle, WA, USA., Pavlovicz RE; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA., Pethe M; Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, NJ, USA.; Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA., Pierce BG; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA., Pilla KB; Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia., Raveh B; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Renfrew PD; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA., Burman SSR; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA., Rubenstein A; Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.; Computational Biology and Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA., Sauer MF; Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA., Scheck A; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Schief W; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Schueler-Furman O; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Sedan Y; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Sevy AM; Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA., Sgourakis NG; Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA., Shi L; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Siegel JB; Department of Chemistry, University of California, Davis, Davis, CA, USA.; Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California, USA.; Genome Center, University of California, Davis, Davis, CA, USA., Silva DA; Department of Biochemistry, University of Washington, Seattle, WA, USA., Smith S; Department of Chemistry, Vanderbilt University, Nashville, TN, USA., Song Y; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA., Stein A; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Szegedy M; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA., Teets FD; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Thyme SB; Department of Biochemistry, University of Washington, Seattle, WA, USA., Wang RY; Department of Biochemistry, University of Washington, Seattle, WA, USA., Watkins A; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA., Zimmerman L; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Bonneau R; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Bonneau@nyu.edu.; Department of Biology, New York University, New York, New York, USA. Bonneau@nyu.edu.; Department of Computer Science, New York University, New York, NY, USA. Bonneau@nyu.edu.; Center for Data Science, New York University, New York, NY, USA. Bonneau@nyu.edu.
Source: Nature methods [Nat Methods] 2020 Jul; Vol. 17 (7), pp. 665-680. Date of Electronic Publication: 2020 Jun 01.
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.; Review
Journal Info: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE
Database: MEDLINE Ultimate
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DbLabel: MEDLINE Ultimate
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  Data: Macromolecular modeling and design in Rosetta: recent methods and frameworks.
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  Data: <searchLink fieldCode="AU" term="%22Leman+JK%22">Leman JK</searchLink>; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Julia.koehler.leman@nyu.edu.; Department of Biology, New York University, New York, New York, USA. Julia.koehler.leman@nyu.edu.<br /><searchLink fieldCode="AU" term="%22Weitzner+BD%22">Weitzner BD</searchLink>; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Lyell Immunopharma Inc., Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Lewis+SM%22">Lewis SM</searchLink>; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Biochemistry, Duke University, Durham, NC, USA.; Cyrus Biotechnology, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Adolf-Bryfogle+J%22">Adolf-Bryfogle J</searchLink>; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.<br /><searchLink fieldCode="AU" term="%22Alam+N%22">Alam N</searchLink>; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.<br /><searchLink fieldCode="AU" term="%22Alford+RF%22">Alford RF</searchLink>; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.<br /><searchLink fieldCode="AU" term="%22Aprahamian+M%22">Aprahamian M</searchLink>; Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA.<br /><searchLink fieldCode="AU" term="%22Baker+D%22">Baker D</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Barlow+KA%22">Barlow KA</searchLink>; Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA, USA.<br /><searchLink fieldCode="AU" term="%22Barth+P%22">Barth P</searchLink>; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA.<br /><searchLink fieldCode="AU" term="%22Basanta+B%22">Basanta B</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Biological Physics Structure and Design PhD Program, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Bender+BJ%22">Bender BJ</searchLink>; Department of Pharmacology, Vanderbilt University, Nashville, TN, USA.<br /><searchLink fieldCode="AU" term="%22Blacklock+K%22">Blacklock K</searchLink>; Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.<br /><searchLink fieldCode="AU" term="%22Bonet+J%22">Bonet J</searchLink>; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Boyken+SE%22">Boyken SE</searchLink>; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Lyell Immunopharma Inc., Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Bradley+P%22">Bradley P</searchLink>; Fred Hutchinson Cancer Research Center, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Bystroff+C%22">Bystroff C</searchLink>; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA.<br /><searchLink fieldCode="AU" term="%22Conway+P%22">Conway P</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Cooper+S%22">Cooper S</searchLink>; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.<br /><searchLink fieldCode="AU" term="%22Correia+BE%22">Correia BE</searchLink>; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Coventry+B%22">Coventry B</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Das+R%22">Das R</searchLink>; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.<br /><searchLink fieldCode="AU" term="%22De+Jong+RM%22">De Jong RM</searchLink>; DSM Biotechnology Center, Delft, the Netherlands.<br /><searchLink fieldCode="AU" term="%22DiMaio+F%22">DiMaio F</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Dsilva+L%22">Dsilva L</searchLink>; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.<br /><searchLink fieldCode="AU" term="%22Dunbrack+R%22">Dunbrack R</searchLink>; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA.<br /><searchLink fieldCode="AU" term="%22Ford+AS%22">Ford AS</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Frenz+B%22">Frenz B</searchLink>; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Fu+DY%22">Fu DY</searchLink>; Department of Chemistry, Vanderbilt University, Nashville, TN, USA.<br /><searchLink fieldCode="AU" term="%22Geniesse+C%22">Geniesse C</searchLink>; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.<br /><searchLink fieldCode="AU" term="%22Goldschmidt+L%22">Goldschmidt L</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Gowthaman+R%22">Gowthaman R</searchLink>; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA.<br /><searchLink fieldCode="AU" term="%22Gray+JJ%22">Gray JJ</searchLink>; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA.<br /><searchLink fieldCode="AU" term="%22Gront+D%22">Gront D</searchLink>; Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland.<br /><searchLink fieldCode="AU" term="%22Guffy+S%22">Guffy S</searchLink>; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.<br /><searchLink fieldCode="AU" term="%22Horowitz+S%22">Horowitz S</searchLink>; Department of Chemistry & Biochemistry, University of Denver, Denver, CO, USA.; The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA.<br /><searchLink fieldCode="AU" term="%22Huang+PS%22">Huang PS</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Huber+T%22">Huber T</searchLink>; Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia.<br /><searchLink fieldCode="AU" term="%22Jacobs+TM%22">Jacobs TM</searchLink>; Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.<br /><searchLink fieldCode="AU" term="%22Jeliazkov+JR%22">Jeliazkov JR</searchLink>; 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Institute of 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.; Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, NJ, USA.; Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.; Computational Biology and Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.<br /><searchLink fieldCode="AU" term="%22Khatib+F%22">Khatib F</searchLink>; Department of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, MA, USA.<br /><searchLink fieldCode="AU" term="%22Khramushin+A%22">Khramushin A</searchLink>; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.<br /><searchLink fieldCode="AU" term="%22King+IC%22">King IC</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Kleffner+R%22">Kleffner R</searchLink>; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.<br /><searchLink fieldCode="AU" term="%22Koepnick+B%22">Koepnick B</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Kortemme+T%22">Kortemme T</searchLink>; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.<br /><searchLink fieldCode="AU" term="%22Kuenze+G%22">Kuenze G</searchLink>; Department of Chemistry, Vanderbilt University, Nashville, TN, USA.; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.<br /><searchLink fieldCode="AU" term="%22Kuhlman+B%22">Kuhlman B</searchLink>; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.<br /><searchLink fieldCode="AU" term="%22Kuroda+D%22">Kuroda D</searchLink>; Medical Device Development and Regulation Research Center, School of Engineering, University of Tokyo, Tokyo, Japan.; Department of Bioengineering, School of Engineering, University of Tokyo, Tokyo, Japan.<br /><searchLink fieldCode="AU" term="%22Labonte+JW%22">Labonte JW</searchLink>; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.; Department of Chemistry, Franklin & Marshall College, Lancaster, PA, USA.<br /><searchLink fieldCode="AU" term="%22Lai+JK%22">Lai JK</searchLink>; Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA.<br /><searchLink fieldCode="AU" term="%22Lapidoth+G%22">Lapidoth G</searchLink>; Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.<br /><searchLink fieldCode="AU" term="%22Leaver-Fay+A%22">Leaver-Fay A</searchLink>; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.<br /><searchLink fieldCode="AU" term="%22Lindert+S%22">Lindert S</searchLink>; Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA.<br /><searchLink fieldCode="AU" term="%22Linsky+T%22">Linsky T</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22London+N%22">London N</searchLink>; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.<br /><searchLink fieldCode="AU" term="%22Lubin+JH%22">Lubin JH</searchLink>; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.<br /><searchLink fieldCode="AU" term="%22Lyskov+S%22">Lyskov S</searchLink>; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.<br /><searchLink fieldCode="AU" term="%22Maguire+J%22">Maguire J</searchLink>; Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.<br /><searchLink fieldCode="AU" term="%22Malmström+L%22">Malmström L</searchLink>; Swiss Institute of Bioinformatics, Lausanne, Switzerland.; Institute for Computational Science, University of Zurich, Zurich, Switzerland.; S3IT, University of Zurich, Zurich, Switzerland.; Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden.<br /><searchLink fieldCode="AU" term="%22Marcos+E%22">Marcos E</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain.<br /><searchLink fieldCode="AU" term="%22Marcu+O%22">Marcu O</searchLink>; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.<br /><searchLink fieldCode="AU" term="%22Marze+NA%22">Marze NA</searchLink>; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.<br /><searchLink fieldCode="AU" term="%22Meiler+J%22">Meiler J</searchLink>; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.; Departments of Chemistry, Pharmacology and Biomedical Informatics, Vanderbilt University, Nashville, TN, USA.; Institute for Chemical Biology, Vanderbilt University, Nashville, TN, USA.<br /><searchLink fieldCode="AU" term="%22Moretti+R%22">Moretti R</searchLink>; Department of Chemistry, Vanderbilt University, Nashville, TN, USA.<br /><searchLink fieldCode="AU" term="%22Mulligan+VK%22">Mulligan VK</searchLink>; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Nerli+S%22">Nerli S</searchLink>; Department of Computer Science, University of California Santa Cruz, Santa Cruz, CA, USA.<br /><searchLink fieldCode="AU" term="%22Norn+C%22">Norn C</searchLink>; Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.<br /><searchLink fieldCode="AU" term="%22Ó'Conchúir+S%22">Ó'Conchúir S</searchLink>; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.<br /><searchLink fieldCode="AU" term="%22Ollikainen+N%22">Ollikainen N</searchLink>; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.<br /><searchLink fieldCode="AU" term="%22Ovchinnikov+S%22">Ovchinnikov S</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Pacella+MS%22">Pacella MS</searchLink>; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.<br /><searchLink fieldCode="AU" term="%22Pan+X%22">Pan X</searchLink>; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.<br /><searchLink fieldCode="AU" term="%22Park+H%22">Park H</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Pavlovicz+RE%22">Pavlovicz RE</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Pethe+M%22">Pethe M</searchLink>; Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, NJ, USA.; Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.<br /><searchLink fieldCode="AU" term="%22Pierce+BG%22">Pierce BG</searchLink>; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA.<br /><searchLink fieldCode="AU" term="%22Pilla+KB%22">Pilla KB</searchLink>; Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia.<br /><searchLink fieldCode="AU" term="%22Raveh+B%22">Raveh B</searchLink>; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.<br /><searchLink fieldCode="AU" term="%22Renfrew+PD%22">Renfrew PD</searchLink>; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.<br /><searchLink fieldCode="AU" term="%22Burman+SSR%22">Burman SSR</searchLink>; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.<br /><searchLink fieldCode="AU" term="%22Rubenstein+A%22">Rubenstein A</searchLink>; Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.; Computational Biology and Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.<br /><searchLink fieldCode="AU" term="%22Sauer+MF%22">Sauer MF</searchLink>; Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA.<br /><searchLink fieldCode="AU" term="%22Scheck+A%22">Scheck A</searchLink>; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland.<br /><searchLink fieldCode="AU" term="%22Schief+W%22">Schief W</searchLink>; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.<br /><searchLink fieldCode="AU" term="%22Schueler-Furman+O%22">Schueler-Furman O</searchLink>; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.<br /><searchLink fieldCode="AU" term="%22Sedan+Y%22">Sedan Y</searchLink>; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.<br /><searchLink fieldCode="AU" term="%22Sevy+AM%22">Sevy AM</searchLink>; Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA.<br /><searchLink fieldCode="AU" term="%22Sgourakis+NG%22">Sgourakis NG</searchLink>; Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA.<br /><searchLink fieldCode="AU" term="%22Shi+L%22">Shi L</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Siegel+JB%22">Siegel JB</searchLink>; Department of Chemistry, University of California, Davis, Davis, CA, USA.; Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California, USA.; Genome Center, University of California, Davis, Davis, CA, USA.<br /><searchLink fieldCode="AU" term="%22Silva+DA%22">Silva DA</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Smith+S%22">Smith S</searchLink>; Department of Chemistry, Vanderbilt University, Nashville, TN, USA.<br /><searchLink fieldCode="AU" term="%22Song+Y%22">Song Y</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Stein+A%22">Stein A</searchLink>; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.<br /><searchLink fieldCode="AU" term="%22Szegedy+M%22">Szegedy M</searchLink>; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.<br /><searchLink fieldCode="AU" term="%22Teets+FD%22">Teets FD</searchLink>; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.<br /><searchLink fieldCode="AU" term="%22Thyme+SB%22">Thyme SB</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Wang+RY%22">Wang RY</searchLink>; Department of Biochemistry, University of Washington, Seattle, WA, USA.<br /><searchLink fieldCode="AU" term="%22Watkins+A%22">Watkins A</searchLink>; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.<br /><searchLink fieldCode="AU" term="%22Zimmerman+L%22">Zimmerman L</searchLink>; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.<br /><searchLink fieldCode="AU" term="%22Bonneau+R%22">Bonneau R</searchLink>; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Bonneau@nyu.edu.; Department of Biology, New York University, New York, New York, USA. Bonneau@nyu.edu.; Department of Computer Science, New York University, New York, NY, USA. Bonneau@nyu.edu.; Center for Data Science, New York University, New York, NY, USA. Bonneau@nyu.edu.
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  Data: <searchLink fieldCode="JN" term="%22101215604%22">Nature methods</searchLink> [Nat Methods] 2020 Jul; Vol. 17 (7), pp. 665-680. <i>Date of Electronic Publication: </i>2020 Jun 01.
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  Data: 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.; Review
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  Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22Nature+Pub%2E+Group%22">Nature Pub. Group </searchLink><i>Country of Publication: </i>United States <i>NLM ID: </i>101215604 <i>Publication Model: </i>Print-Electronic <i>Cited Medium: </i>Internet <i>ISSN: </i>1548-7105 (Electronic) <i>Linking ISSN: </i><searchLink fieldCode="IS" term="%2215487091%22">15487091 </searchLink><i>NLM ISO Abbreviation: </i>Nat Methods <i>Subsets: </i>MEDLINE
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      – TitleFull: Macromolecular modeling and design in Rosetta: recent methods and frameworks.
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            NameFull: Zimmerman L
      – PersonEntity:
          Name:
            NameFull: Bonneau R
    IsPartOfRelationships:
      – BibEntity:
          Dates:
            – D: 01
              M: 07
              Text: 2020 Jul
              Type: published
              Y: 2020
          Identifiers:
            – Type: issn-electronic
              Value: 1548-7105
          Numbering:
            – Type: volume
              Value: 17
            – Type: issue
              Value: 7
          Titles:
            – TitleFull: Nature methods
              Type: main
ResultId 1