Multi-state design of flexible proteins predicts sequences optimal for conformational change.

Autor: Marion F Sauer, Alexander M Sevy, James E Crowe, Jens Meiler

Publikováno v: PLoS Computational Biology, Vol 16, Iss 2, p e1007339 (2020)

Computational protein design of an ensemble of conformations for one protein-i.e., multi-state design-determines the side chain identity by optimizing the energetic contributions of that side chain in each of the backbone conformations. Sampling the

Externí odkaz: https://doaj.org/article/b1aa77a247d148a0864db512bb676137

Macromolecular modeling and design in Rosetta: recent methods and frameworks

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

Publikováno v: Nat Methods

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=doi_dedup___::c561276e840d68005d2aab06fb9642da
https://pubmed.ncbi.nlm.nih.gov/32483333

Protocols for Molecular Modeling with Rosetta3 and RosettaScripts

Autor: Marion F. Sauer, Jens Meiler, Frank DiMaio, Rocco Moretti, Alyssa D. Lokits, Darwin Y. Fu, Amanda M. Duran, Benjamin K. Mueller, Gregory Sliwoski, Alberto Cisneros, Jessica A. Finn, Alexander M. Sevy, Jonathan H. Sheehan, Amandeep K. Sangha, Brian J. Bender

Publikováno v: Biochemistry

Previously, we published an article providing an overview of the Rosetta suite of biomacromolecular modeling software and a series of step-by-step tutorials [Kaufmann, K. W., et al. (2010) Biochemistry 49, 2987–2998]. The overwhelming positive resp

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6ae953ac02b361c237cb3fd923e8a347
https://pubmed.ncbi.nlm.nih.gov/27490953

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

Autor: Samuel Schmitz, Marion F. Sauer, Georg Kuenze, Jens Meiler, Cristina Martina, Amandeep K. Sangha, Brian J. Bender, Bruno E. Correia, Shannon T. Smith, Diego del Alamo, Alican Gulsevin, Hope Woods, Pranav Kodali, Clara T. Schoeder, Benjamin K. Mueller, Nina G. Bozhanova, Jared Adolf-Bryfogle, Jonathan H. Sheehan, Alexander M. Sevy, Jessica A. Finn, Jaume Bonet, James E. Crowe, Rocco Moretti, William R. Schief, Brennica Marlow

Publikováno v: Biochemistry

Structure-based antibody and antigen design has advanced greatly in recent years, due not only to the increasing availability of experimentally determined structures but also to improved computational methods for both prediction and design. Constant

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ac4ff1823829bd33bde6ce33f3b42afd
https://infoscience.epfl.ch/record/285560