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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;
- 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;
- Stein, Amelie;
- Szegedy, Maria;
- Teets, Frank D;
- Thyme, Summer B;
- Wang, Ray Yu-Ruei;
- Watkins, Andrew;
- Zimmerman, Lior;
- Bonneau, Richard
- et al.
Published Web Location
https://doi.org/10.1038/s41592-020-0848-2Abstract
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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