Macromolecular modeling and design in Rosetta: recent methods and frameworks.
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ABSTRACT:
SUBMITTER: Leman JK
PROVIDER: S-EPMC7603796 | biostudies-literature | 2020 Jul
REPOSITORIES: biostudies-literature
Publications
Macromolecular modeling and design in Rosetta: recent methods and frameworks.
Leman Julia Koehler JK Weitzner Brian D BD Lewis Steven M SM Adolf-Bryfogle Jared J Alam Nawsad N Alford Rebecca F RF Aprahamian Melanie M Baker David D Barlow Kyle A KA Barth Patrick P Basanta Benjamin B Bender Brian J BJ Blacklock Kristin K Bonet Jaume J Boyken Scott E SE Bradley Phil P Bystroff Chris C Conway Patrick P Cooper Seth S Correia Bruno E BE Coventry Brian B Das Rhiju R De Jong René M RM DiMaio Frank F Dsilva Lorna L Dunbrack Roland R Ford Alexander S AS Frenz Brandon B Fu Darwin Y DY Geniesse Caleb C Goldschmidt Lukasz L Gowthaman Ragul R Gray Jeffrey J JJ Gront Dominik D Guffy Sharon S Horowitz Scott S Huang Po-Ssu PS Huber Thomas T Jacobs Tim M TM Jeliazkov Jeliazko R JR Johnson David K DK Kappel Kalli K Karanicolas John J Khakzad Hamed H Khar Karen R KR Khare Sagar D SD Khatib Firas F Khramushin Alisa A King Indigo C IC Kleffner Robert R Koepnick Brian B Kortemme Tanja T Kuenze Georg G Kuhlman Brian B Kuroda Daisuke D Labonte Jason W JW Lai Jason K JK Lapidoth Gideon G Leaver-Fay Andrew A Lindert Steffen S Linsky Thomas T London Nir N Lubin Joseph H JH Lyskov Sergey S Maguire Jack J Malmström Lars L Marcos Enrique E Marcu Orly O Marze Nicholas A NA Meiler Jens J Moretti Rocco R Mulligan Vikram Khipple VK Nerli Santrupti S Norn Christoffer C Ó'Conchúir Shane S Ollikainen Noah N Ovchinnikov Sergey S Pacella Michael S MS Pan Xingjie X Park Hahnbeom H Pavlovicz Ryan E RE Pethe Manasi M Pierce Brian G BG Pilla Kala Bharath KB Raveh Barak B Renfrew P Douglas PD Burman Shourya S Roy SSR Rubenstein Aliza A Sauer Marion F MF Scheck Andreas A Schief William W Schueler-Furman Ora O Sedan Yuval Y Sevy Alexander M AM Sgourakis Nikolaos G NG Shi Lei L Siegel Justin B JB Silva Daniel-Adriano DA Smith Shannon S Song Yifan Y Stein Amelie A Szegedy Maria M Teets Frank D FD Thyme Summer B SB Wang Ray Yu-Ruei RY Watkins Andrew A Zimmerman Lior L Bonneau Richard R
Nature methods 20200601 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 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 ...[more]
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