Macromolecular modeling and design in Rosetta: recent methods and frameworks

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

NATURE METHODS（2020）

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摘要

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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关键词

Computational biophysics,Protein design,Protein structure predictions,Software,Life Sciences,general,Biological Techniques,Biological Microscopy,Biomedical Engineering/Biotechnology,Bioinformatics,Proteomics

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