Macromolecular modeling and design in Rosetta: recent methods and frameworks

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

doi:10.1038/s41592-020-0848-2

Macromolecular modeling and design in Rosetta: recent methods and frameworks

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

Biochemistry and Molecular Medicine

Research output: Contribution to journal › Article › peer-review

20 Scopus citations

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	https://doi.org/10.1038/s41592-020-0848-2
State	Accepted/In press - Jan 1 2020

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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Leman, J. K., Weitzner, B. D., Lewis, S. M., Adolf-Bryfogle, J., Alam, N., Alford, R. F., Aprahamian, M., Baker, D., Barlow, K. A., Barth, P., Basanta, B., Bender, B. J., Blacklock, K., Bonet, J., Boyken, S. E., Bradley, P., Bystroff, C., Conway, P., Cooper, S., ... Bonneau, R. (Accepted/In press). Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. https://doi.org/10.1038/s41592-020-0848-2

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

Leman, JK, Weitzner, BD, Lewis, SM, Adolf-Bryfogle, J, Alam, N, Alford, RF, Aprahamian, M, Baker, D, Barlow, KA, Barth, P, Basanta, B, Bender, BJ, Blacklock, K, Bonet, J, Boyken, SE, Bradley, P, Bystroff, C, Conway, P, Cooper, S, Correia, BE, Coventry, B, Das, R, De Jong, RM, DiMaio, F, Dsilva, L, Dunbrack, R, Ford, AS, Frenz, B, Fu, DY, Geniesse, C, Goldschmidt, L, Gowthaman, R, Gray, JJ, Gront, D, Guffy, S, Horowitz, S, Huang, PS, Huber, T, Jacobs, TM, Jeliazkov, JR, Johnson, DK, Kappel, K, Karanicolas, J, Khakzad, H, Khar, KR, Khare, SD, Khatib, F, Khramushin, A, King, IC, Kleffner, R, Koepnick, B, Kortemme, T, Kuenze, G, Kuhlman, B, Kuroda, D, Labonte, JW, Lai, JK, Lapidoth, G, Leaver-Fay, A, Lindert, S, Linsky, T, London, N, Lubin, JH, Lyskov, S, Maguire, J, Malmström, L, Marcos, E, Marcu, O, Marze, NA, Meiler, J, Moretti, R, Mulligan, VK, Nerli, S, Norn, C, Ó’Conchúir, S, Ollikainen, N, Ovchinnikov, S, Pacella, MS, Pan, X, Park, H, Pavlovicz, RE, Pethe, M, Pierce, BG, Pilla, KB, Raveh, B, Renfrew, PD, Burman, SSR, Rubenstein, A, Sauer, MF, Scheck, A, Schief, W, Schueler-Furman, O, Sedan, Y, Sevy, AM, Sgourakis, NG, Shi, L, Siegel, JB, Silva, DA, Smith, S, Song, Y, Stein, A, Szegedy, M, Teets, FD, Thyme, SB, Wang, RYR, Watkins, A, Zimmerman, L & Bonneau, R 2020, 'Macromolecular modeling and design in Rosetta: recent methods and frameworks', Nature Methods. https://doi.org/10.1038/s41592-020-0848-2

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. / Macromolecular modeling and design in Rosetta : recent methods and frameworks. In: Nature Methods. 2020.

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AU - Adolf-Bryfogle, Jared

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AU - Alford, Rebecca F.

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AU - Baker, David

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AU - Barth, Patrick

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AU - Boyken, Scott E.

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AU - Dsilva, Lorna

AU - Dunbrack, Roland

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AU - Frenz, Brandon

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AU - Geniesse, Caleb

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AU - Gowthaman, Ragul

AU - Gray, Jeffrey J.

AU - Gront, Dominik

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AU - Horowitz, Scott

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AU - Huber, Thomas

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AU - Kuenze, Georg

AU - Kuhlman, Brian

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AU - Lai, Jason K.

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AU - Leaver-Fay, Andrew

AU - Lindert, Steffen

AU - Linsky, Thomas

AU - London, Nir

AU - Lubin, Joseph H.

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AU - Maguire, Jack

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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

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