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 http://www.rosettacommons.org.
Original language | English (US) |
---|---|
Journal | Nature Methods |
DOIs | |
State | Accepted/In press - Jan 1 2020 |
ASJC Scopus subject areas
- Biotechnology
- Biochemistry
- Molecular Biology
- Cell Biology
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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.
In: Nature Methods, 01.01.2020.Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - Macromolecular modeling and design in Rosetta
T2 - recent methods and frameworks
AU - Leman, Julia Koehler
AU - Weitzner, Brian D.
AU - Lewis, Steven M.
AU - Adolf-Bryfogle, Jared
AU - Alam, Nawsad
AU - Alford, Rebecca F.
AU - Aprahamian, Melanie
AU - Baker, David
AU - Barlow, Kyle A.
AU - Barth, Patrick
AU - Basanta, Benjamin
AU - Bender, Brian J.
AU - Blacklock, Kristin
AU - Bonet, Jaume
AU - Boyken, Scott E.
AU - Bradley, Phil
AU - Bystroff, Chris
AU - Conway, Patrick
AU - Cooper, Seth
AU - Correia, Bruno E.
AU - Coventry, Brian
AU - Das, Rhiju
AU - De Jong, René M.
AU - DiMaio, Frank
AU - Dsilva, Lorna
AU - Dunbrack, Roland
AU - Ford, Alexander S.
AU - Frenz, Brandon
AU - Fu, Darwin Y.
AU - Geniesse, Caleb
AU - Goldschmidt, Lukasz
AU - Gowthaman, Ragul
AU - Gray, Jeffrey J.
AU - Gront, Dominik
AU - Guffy, Sharon
AU - Horowitz, Scott
AU - Huang, Po Ssu
AU - Huber, Thomas
AU - Jacobs, Tim M.
AU - Jeliazkov, Jeliazko R.
AU - Johnson, David K.
AU - Kappel, Kalli
AU - Karanicolas, John
AU - Khakzad, Hamed
AU - Khar, Karen R.
AU - Khare, Sagar D.
AU - Khatib, Firas
AU - Khramushin, Alisa
AU - King, Indigo C.
AU - Kleffner, Robert
AU - Koepnick, Brian
AU - Kortemme, Tanja
AU - Kuenze, Georg
AU - Kuhlman, Brian
AU - Kuroda, Daisuke
AU - Labonte, Jason W.
AU - Lai, Jason K.
AU - Lapidoth, Gideon
AU - Leaver-Fay, Andrew
AU - Lindert, Steffen
AU - Linsky, Thomas
AU - London, Nir
AU - Lubin, Joseph H.
AU - Lyskov, Sergey
AU - Maguire, Jack
AU - Malmström, Lars
AU - Marcos, Enrique
AU - Marcu, Orly
AU - Marze, Nicholas A.
AU - Meiler, Jens
AU - Moretti, Rocco
AU - Mulligan, Vikram Khipple
AU - Nerli, Santrupti
AU - Norn, Christoffer
AU - Ó’Conchúir, Shane
AU - Ollikainen, Noah
AU - Ovchinnikov, Sergey
AU - Pacella, Michael S.
AU - Pan, Xingjie
AU - Park, Hahnbeom
AU - Pavlovicz, Ryan E.
AU - Pethe, Manasi
AU - Pierce, Brian G.
AU - Pilla, Kala Bharath
AU - Raveh, Barak
AU - Renfrew, P. Douglas
AU - Burman, Shourya S.Roy
AU - Rubenstein, Aliza
AU - Sauer, Marion F.
AU - Scheck, Andreas
AU - Schief, William
AU - Schueler-Furman, Ora
AU - Sedan, Yuval
AU - Sevy, Alexander M.
AU - Sgourakis, Nikolaos G.
AU - Shi, Lei
AU - Siegel, Justin B.
AU - Silva, Daniel Adriano
AU - Smith, Shannon
AU - Song, Yifan
AU - Stein, Amelie
AU - Szegedy, Maria
AU - Teets, Frank D.
AU - Thyme, Summer B.
AU - Wang, Ray Yu Ruei
AU - Watkins, Andrew
AU - Zimmerman, Lior
AU - Bonneau, Richard
PY - 2020/1/1
Y1 - 2020/1/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85085875871&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85085875871&partnerID=8YFLogxK
U2 - 10.1038/s41592-020-0848-2
DO - 10.1038/s41592-020-0848-2
M3 - Article
C2 - 32483333
AN - SCOPUS:85085875871
JO - Nature Methods
JF - Nature Methods
SN - 1548-7091
ER -