Macromolecular modeling and design in Rosetta: recent methods and frameworks

Autor: Leman, Julia Koehler, Weitzner, Brian D, Lewis, Steven M, Adolf-Bryfogle, Jared, Alam, Nawsad, Alford, Rebecca F, Aprahamian, Melanie, Baker, David, Barlow, Kyle A, Barth, Patrick, Basanta, Benjamin, Bender, Brian J, Blacklock, Kristin, Bonet, Jaume, Boyken, Scott E, Bradley, Phil, Bystroff, Chris, Conway, Patrick, Cooper, Seth, Correia, Bruno E, Coventry, Brian, Das, Rhiju, De Jong, René M, DiMaio, Frank, Dsilva, Lorna, Dunbrack, Roland, Ford, Alexander S, Frenz, Brandon, Fu, Darwin Y, Geniesse, Caleb, Goldschmidt, Lukasz, Gowthaman, Ragul, Gray, Jeffrey J, Gront, Dominik, Guffy, Sharon, Horowitz, Scott, Huang, Po-Ssu, Huber, Thomas, Jacobs, Tim M, Jeliazkov, Jeliazko R, Johnson, David K, Kappel, Kalli, Karanicolas, John, Khakzad, Hamed, Khar, Karen R, Khare, Sagar D, Khatib, Firas, Khramushin, Alisa, King, Indigo C, Kleffner, Robert, Koepnick, Brian, Kortemme, Tanja, Kuenze, Georg, Kuhlman, Brian, Kuroda, Daisuke, Labonte, Jason W, Lai, Jason K, Lapidoth, Gideon, Leaver-Fay, Andrew, Lindert, Steffen, Linsky, Thomas, London, Nir, Lubin, Joseph H, Lyskov, Sergey, Maguire, Jack, Malmström, Lars, Marcos, Enrique, Marcu, Orly, Marze, Nicholas A, Meiler, Jens, Moretti, Rocco, Mulligan, Vikram Khipple, Nerli, Santrupti, Norn, Christoffer, Ó'Conchúir, Shane, Ollikainen, Noah, Ovchinnikov, Sergey, Pacella, Michael S, Pan, Xingjie, Park, Hahnbeom, Pavlovicz, Ryan E, Pethe, Manasi, Pierce, Brian G, Pilla, Kala Bharath, Raveh, Barak, Renfrew, P Douglas, Burman, Shourya S Roy, Rubenstein, Aliza, Sauer, Marion F, Scheck, Andreas, Schief, William, Schueler-Furman, Ora, Sedan, Yuval, Sevy, Alexander M, Sgourakis, Nikolaos G, Shi, Lei, Siegel, Justin B, Silva, Daniel-Adriano, Smith, Shannon, Song, Yifan

Publikováno v: Nature methods, vol 17, iss 7

The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactore

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=od_______325::0fdd55bd8749c268988feeaaf1d38de5
https://escholarship.org/uc/item/646416k5

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

Autor: 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.

Publikováno v: Nature methods [Nat Methods] 2020 Jul; Vol. 17 (7), pp. 665-680. Date of Electronic Publication: 2020 Jun 01.