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, Rene 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; Malmstroem, Lars; Marcos, Enrique; Marcu, Orly; Marze, Nicholas A.; Meiler, Jens; Moretti, Rocco; Mulligan, Vikram Khipple; Nerli, Santrupti; Norn, Christoffer; O'Conchuir, 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
2020
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 .
This Perspective reviews tools developed over the past five years in the macromolecular modeling, docking and design software Rosetta.
This Perspective reviews tools developed over the past five years in the macromolecular modeling, docking and design software Rosetta.
Details
Title
Macromolecular modeling and design in Rosetta: recent methods and frameworks
Author(s)
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, Rene 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 ; Malmstroem, Lars ; Marcos, Enrique ; Marcu, Orly ; Marze, Nicholas A. ; Meiler, Jens ; Moretti, Rocco ; Mulligan, Vikram Khipple ; Nerli, Santrupti ; Norn, Christoffer ; O'Conchuir, 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
Published in
Nature Methods
Volume
17
Pages
665–680
Date
2020-06-01
Publisher
London, NATURE PUBLISHING GROUP
ISSN
1548-7091
1548-7105
1548-7105
Keywords
Other identifier(s)
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Record Appears in
Scientific production and competences > STI - School of Engineering > IBI-STI - Interfaculty Institute of Bioengineering > LPDI - Laboratory of Protein Design and Immunoengineering
Scientific production and competences > SV - School of Life Sciences > IBI-SV - Interfaculty Institute of Bioengineering > UPBARTH - Laboratory of Protein and Cell Engineering
Peer-reviewed publications
Work produced at EPFL
Journal Articles
Published
Scientific production and competences > SV - School of Life Sciences > IBI-SV - Interfaculty Institute of Bioengineering > UPBARTH - Laboratory of Protein and Cell Engineering
Peer-reviewed publications
Work produced at EPFL
Journal Articles
Published
Record creation date
2020-06-14