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^*

^*Corresponding author for this work

Research output: Contribution to journal › Review article › peer-review

449 Citations (Scopus)

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
Pages (from-to)	665-680
Number of pages	16
Journal	Nature Methods
Volume	17
Issue number	7
DOIs	https://doi.org/10.1038/s41592-020-0848-2
Publication status	Published - 1 Jul 2020

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10.1038/s41592-020-0848-2

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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. (2020). Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods, 17(7), 665-680. https://doi.org/10.1038/s41592-020-0848-2

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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.",

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

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doi = "10.1038/s41592-020-0848-2",

language = "English",

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journal = "Nature Methods",

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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, vol. 17, no. 7, pp. 665-680. https://doi.org/10.1038/s41592-020-0848-2

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 - 2020/7/1

Y1 - 2020/7/1

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

U2 - 10.1038/s41592-020-0848-2

DO - 10.1038/s41592-020-0848-2

M3 - Review article

SN - 1548-7091

VL - 17

SP - 665

EP - 680

JO - Nature Methods

JF - Nature Methods

IS - 7

ER -

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Abstract

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