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Macromolecular modeling and design in Rosetta: recent methods and frameworks.
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.
  • Leman JK; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Julia.koehler.leman@nyu.edu.
  • Weitzner BD; Department of Biology, New York University, New York, New York, USA. Julia.koehler.leman@nyu.edu.
  • Lewis SM; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
  • Adolf-Bryfogle J; Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • Alam N; Institute for Protein Design, University of Washington, Seattle, WA, USA.
  • Alford RF; Lyell Immunopharma Inc., Seattle, WA, USA.
  • Aprahamian M; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  • Baker D; Department of Biochemistry, Duke University, Durham, NC, USA.
  • Barlow KA; Cyrus Biotechnology, Seattle, WA, USA.
  • Barth P; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
  • Basanta B; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
  • Bender BJ; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
  • Blacklock K; Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA.
  • Bonet J; Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • Boyken SE; Institute for Protein Design, University of Washington, Seattle, WA, USA.
  • Bradley P; Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA, USA.
  • Bystroff C; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
  • Conway P; Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA.
  • Cooper S; Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • Correia BE; Biological Physics Structure and Design PhD Program, University of Washington, Seattle, WA, USA.
  • Coventry B; Department of Pharmacology, Vanderbilt University, Nashville, TN, USA.
  • Das R; Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
  • De Jong RM; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
  • DiMaio F; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
  • Dsilva L; Institute for Protein Design, University of Washington, Seattle, WA, USA.
  • Dunbrack R; Lyell Immunopharma Inc., Seattle, WA, USA.
  • Ford AS; Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
  • Frenz B; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA.
  • Fu DY; Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • Geniesse C; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
  • Goldschmidt L; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
  • Gowthaman R; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
  • Gray JJ; Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • Gront D; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
  • Guffy S; DSM Biotechnology Center, Delft, the Netherlands.
  • Horowitz S; Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • Huang PS; Institute for Protein Design, University of Washington, Seattle, WA, USA.
  • Huber T; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
  • Jacobs TM; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA.
  • Jeliazkov JR; Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • Johnson DK; Institute for Protein Design, University of Washington, Seattle, WA, USA.
  • Kappel K; Cyrus Biotechnology, Seattle, WA, USA.
  • Karanicolas J; Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
  • Khakzad H; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
  • Khar KR; Department of Biochemistry, University of Washington, Seattle, WA, USA.
  • Khare SD; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.
  • Khatib F; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA.
  • Khramushin A; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
  • King IC; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA.
  • Kleffner R; Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland.
Nat Methods ; 17(7): 665-680, 2020 07.
Article en En | MEDLINE | ID: mdl-32483333
ABSTRACT
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 refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities. Here we review tools developed in the last 5 years, including over 80 methods. We discuss improvements to the score function, user interfaces and usability. Rosetta is available at http//www.rosettacommons.org.
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Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Programas Informáticos / Proteínas / Modelos Moleculares / Sustancias Macromoleculares Tipo de estudio: Prognostic_studies Idioma: En Año: 2020 Tipo del documento: Article
Texto completo
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Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Programas Informáticos / Proteínas / Modelos Moleculares / Sustancias Macromoleculares Tipo de estudio: Prognostic_studies Idioma: En Año: 2020 Tipo del documento: Article