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

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

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)
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
State	Published - Jul 1 2020

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

Access to Document

10.1038/s41592-020-0848-2

Cite this

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

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

@article{d662f847f39349a4bbbacdba1baf8e77,

title = "Macromolecular modeling and design in Rosetta: recent methods and frameworks",

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",

note = "Funding Information: RosettaCommons is supported by NIH R01 GM073151 to B. Kuhlman, NSF, the Packard Foundation, the Beckman Foundation, the Alfred P. Sloan Foundation and the Simons Foundation. This work was also supported by a 100,000,000 CPU-hour donation from Google Inc to P.C. and a 125,760,000 CPU-hour allocation on the Mira and Theta supercomputers through the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program to D.B., F.D., A.L.-F. and V.K.M. This research used resources of the Argonne Leadership Computing Facility, which is a DOE Office of Science user facility supported under Contract DE-AC02-06CH11357. Supported by AHA 18POST34080422 to G.K., AMED J-PRIDE JP18fm0208022h to D.K., the Biltema Foundation to B.E.C. and Boehringer Ingelheim Fonds to C.N.; computing was performed using resources of the Argonne Leadership Computing Facility at Argonne National Laboratory, which is supported by the Office of Science of the United States to P.C.; DFG KU 3510/1-1 to G.K.; DP120100561 to T.H.; DP150100383 to T.H. and K.B.P.; EMBO long-term fellowship ALTF 698-2011 to A. Stein; EPFL-Fellows H2020 Marie Sklodowska-Curie to J.B.; European Research Council Grant 310873 to O.S.-F. and N.A.; European Research Council Grant 310873 to Y. Sedan and O.M.; European Research Council Starting grant 716058 to B.E.C. and A. Scheck; FT0991709 to T.H.; Foundation of Knut and Alice Wallenberg 20160023 to L.M.; a Hertz Foundation Fellowship to R.F.A.; the Howard Hughes Medical Institute to D.B.; Hyak supercomputer system supported in part by the University of Washington eScience Institute to the D.B. and F.D. labs; Israel Science Foundation 2017717 to O.S.-F. and N.A.; Japan Society for the Promotion of Science JP17K18113 to D.K.; MCB1330760 to S.D.K.; Marie Curie International Outgoing Fellowship FP7-PEOPLE-2011-IOF 298976 to E.M.; National Science Centre, Poland, 2018/29/B/ST6/01989 to D.G.; NIAID T32AI007244 to J.A.-B.; NIAID U19 AI117905 to A.M.S.; NIEHS P42ES004699 to J.B.S.; NIGMS Ruth L Kirschstein National Research Service Award T32GM008268 to P.C.; NIGMS T32 GM007628 to B.J.B.; NIH 1R35 GM122579 to R. Das; NSF DMREF award 1728858 and DMR-0820341 to R.B.; NIH 1UH2CA203780 to S.C. and F.K.; NIH 5F32GM110899-02 to T.L.; NIH F31GM123616 to J.R.J.; NIH F32CA189246 to J.W.L.; NIH P01 U19AI117905, R01 AI113867 and UM1 Al100663 to W.S.; NIH R00 GM120388 to S.H.; NIH R01 AI143997 to N.G.S.; NIH R01 DK097376, R01 GM080403, R01 HL122010 and R01 GM099842 to J. Meiler; NIH R01 GM073960, R01 GM117968 and R01067553 to B. Kuhlman; NIH R01 GM076324 to J.B.S.; NIH R01 GM127578 and R01 GM078221 to J.J.G.; NIH R01 GM084453 to R. Dunbrack; NIH R01 GM088277 and R01 GM121487 to P. Bradley; NIH R01 GM092802, R01 GM092802, R01084433 and GM092802 to D.B.; NIH R01 GM098101, R01 GM110089 and R01 GM117189 to T.K.; NIH R01 GM099959 to J.K.; NIH R01 GM123089 to F.D.; NIH R01 GM126299 to B.G.P.; NIH R01 GM099827 to C.B.; NIH R01088277 to S.B.T.; NIH R21 AI121799 to J. Meiler; NIH R21 CA219847 and R21 GM102716 to R. Das; NIH R35 GM122517 to R. Dunbrack; NIH R35 GM125034 to N.G.S.; NIH RL1CA133832 to D.B.; NIH U19 AI117905 to J. Meiler; NIH/NCI Cancer Center support grant P30 CA006927 to J.K.; NSF 1507736 and NSF DMR 1507736 to J.J.G.; NSF 1627539, 1805510 and 1827246 to J.B.S.; NSF 1629879 to S.C.; NSF CHE 1305874, CISE 1629811 and CNS-1629811 to J. Meiler; NSF CHE 1750666 to S. Lindert; NSF DBI-1262182 and DBI-1564692 to T.K.; NSF GRF DGE-1433187 to A.R.; NSF Graduate Research Fellowships to R.F.A., K.K., B. Koepnick and S.B.T.; NSF MCB1330760 and MCB1716623 to S.D.K.; Open Philanthropy to B.C.; PhRMA Informatics Pre-Doctoral Fellowship U22879-001 to S.S.; a PhRMA Foundation Predoctoral Fellowship to D.Y.F.; RosettaCommons to L.G., A.R., F.D., S.C., A.W., M.S., C.G., K.B., R. Das, S.D.K., J. Koehler Leman and K.K.; Career Award at the Scientific Interface from Burroughs Wellcome Fund to S.E.B.; Simons Foundation to V.K.M., R.B., P.D.R. and J. Koehler Leman; a Stanford Graduate Fellowship to K.K.; a Starter Grant from the European Research Council to G.L.; Swiss National Science Foundation – NCCR Molecular Systems Engineering 51NF40-141825 to B.E.C.; Swiss National Science Foundation 310030_163139 to B.E.C.; Swiss National Science Foundation SNF 200021 160188 to L.M. and H.K.; UCSF/UCB Graduate Program in Bioengineering to X.P.; USA-Israel Binational Science Foundation 2009418 to B.R., L.Z. and N.L.; USA-Israel Binational Science Foundation 2009418 and 2015207 to O.S.-F. and N.A.; USA-Israel Binational Science Foundation 2015207 to A.K.; Washington Research Foundation Innovation Postdoctoral Fellowship to B.D.W.; XSEDE, which is supported by NSF ACI-1548562; NIH R01 GM097207 to P. Barth; and the MCB120101 XSEDE allocation to P. Barth. The authors would like to thank Jason C. Klima for his work on PyRosetta. Publisher Copyright: {\textcopyright} 2020, Springer Nature America, Inc.",

year = "2020",

month = jul,

day = "1",

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

language = "English (US)",

volume = "17",

pages = "665--680",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Public Library of Science",

number = "7",

}

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

N1 - Funding Information: RosettaCommons is supported by NIH R01 GM073151 to B. Kuhlman, NSF, the Packard Foundation, the Beckman Foundation, the Alfred P. Sloan Foundation and the Simons Foundation. This work was also supported by a 100,000,000 CPU-hour donation from Google Inc to P.C. and a 125,760,000 CPU-hour allocation on the Mira and Theta supercomputers through the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program to D.B., F.D., A.L.-F. and V.K.M. This research used resources of the Argonne Leadership Computing Facility, which is a DOE Office of Science user facility supported under Contract DE-AC02-06CH11357. Supported by AHA 18POST34080422 to G.K., AMED J-PRIDE JP18fm0208022h to D.K., the Biltema Foundation to B.E.C. and Boehringer Ingelheim Fonds to C.N.; computing was performed using resources of the Argonne Leadership Computing Facility at Argonne National Laboratory, which is supported by the Office of Science of the United States to P.C.; DFG KU 3510/1-1 to G.K.; DP120100561 to T.H.; DP150100383 to T.H. and K.B.P.; EMBO long-term fellowship ALTF 698-2011 to A. Stein; EPFL-Fellows H2020 Marie Sklodowska-Curie to J.B.; European Research Council Grant 310873 to O.S.-F. and N.A.; European Research Council Grant 310873 to Y. Sedan and O.M.; European Research Council Starting grant 716058 to B.E.C. and A. Scheck; FT0991709 to T.H.; Foundation of Knut and Alice Wallenberg 20160023 to L.M.; a Hertz Foundation Fellowship to R.F.A.; the Howard Hughes Medical Institute to D.B.; Hyak supercomputer system supported in part by the University of Washington eScience Institute to the D.B. and F.D. labs; Israel Science Foundation 2017717 to O.S.-F. and N.A.; Japan Society for the Promotion of Science JP17K18113 to D.K.; MCB1330760 to S.D.K.; Marie Curie International Outgoing Fellowship FP7-PEOPLE-2011-IOF 298976 to E.M.; National Science Centre, Poland, 2018/29/B/ST6/01989 to D.G.; NIAID T32AI007244 to J.A.-B.; NIAID U19 AI117905 to A.M.S.; NIEHS P42ES004699 to J.B.S.; NIGMS Ruth L Kirschstein National Research Service Award T32GM008268 to P.C.; NIGMS T32 GM007628 to B.J.B.; NIH 1R35 GM122579 to R. Das; NSF DMREF award 1728858 and DMR-0820341 to R.B.; NIH 1UH2CA203780 to S.C. and F.K.; NIH 5F32GM110899-02 to T.L.; NIH F31GM123616 to J.R.J.; NIH F32CA189246 to J.W.L.; NIH P01 U19AI117905, R01 AI113867 and UM1 Al100663 to W.S.; NIH R00 GM120388 to S.H.; NIH R01 AI143997 to N.G.S.; NIH R01 DK097376, R01 GM080403, R01 HL122010 and R01 GM099842 to J. Meiler; NIH R01 GM073960, R01 GM117968 and R01067553 to B. Kuhlman; NIH R01 GM076324 to J.B.S.; NIH R01 GM127578 and R01 GM078221 to J.J.G.; NIH R01 GM084453 to R. Dunbrack; NIH R01 GM088277 and R01 GM121487 to P. Bradley; NIH R01 GM092802, R01 GM092802, R01084433 and GM092802 to D.B.; NIH R01 GM098101, R01 GM110089 and R01 GM117189 to T.K.; NIH R01 GM099959 to J.K.; NIH R01 GM123089 to F.D.; NIH R01 GM126299 to B.G.P.; NIH R01 GM099827 to C.B.; NIH R01088277 to S.B.T.; NIH R21 AI121799 to J. Meiler; NIH R21 CA219847 and R21 GM102716 to R. Das; NIH R35 GM122517 to R. Dunbrack; NIH R35 GM125034 to N.G.S.; NIH RL1CA133832 to D.B.; NIH U19 AI117905 to J. Meiler; NIH/NCI Cancer Center support grant P30 CA006927 to J.K.; NSF 1507736 and NSF DMR 1507736 to J.J.G.; NSF 1627539, 1805510 and 1827246 to J.B.S.; NSF 1629879 to S.C.; NSF CHE 1305874, CISE 1629811 and CNS-1629811 to J. Meiler; NSF CHE 1750666 to S. Lindert; NSF DBI-1262182 and DBI-1564692 to T.K.; NSF GRF DGE-1433187 to A.R.; NSF Graduate Research Fellowships to R.F.A., K.K., B. Koepnick and S.B.T.; NSF MCB1330760 and MCB1716623 to S.D.K.; Open Philanthropy to B.C.; PhRMA Informatics Pre-Doctoral Fellowship U22879-001 to S.S.; a PhRMA Foundation Predoctoral Fellowship to D.Y.F.; RosettaCommons to L.G., A.R., F.D., S.C., A.W., M.S., C.G., K.B., R. Das, S.D.K., J. Koehler Leman and K.K.; Career Award at the Scientific Interface from Burroughs Wellcome Fund to S.E.B.; Simons Foundation to V.K.M., R.B., P.D.R. and J. Koehler Leman; a Stanford Graduate Fellowship to K.K.; a Starter Grant from the European Research Council to G.L.; Swiss National Science Foundation – NCCR Molecular Systems Engineering 51NF40-141825 to B.E.C.; Swiss National Science Foundation 310030_163139 to B.E.C.; Swiss National Science Foundation SNF 200021 160188 to L.M. and H.K.; UCSF/UCB Graduate Program in Bioengineering to X.P.; USA-Israel Binational Science Foundation 2009418 to B.R., L.Z. and N.L.; USA-Israel Binational Science Foundation 2009418 and 2015207 to O.S.-F. and N.A.; USA-Israel Binational Science Foundation 2015207 to A.K.; Washington Research Foundation Innovation Postdoctoral Fellowship to B.D.W.; XSEDE, which is supported by NSF ACI-1548562; NIH R01 GM097207 to P. Barth; and the MCB120101 XSEDE allocation to P. Barth. The authors would like to thank Jason C. Klima for his work on PyRosetta. Publisher Copyright: © 2020, Springer Nature America, Inc.

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

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 - Review article

C2 - 32483333

AN - SCOPUS:85085875871

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

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