Rosetta3: An object-oriented software suite for the simulation and design of macromolecules

Andrew Leaver-Fay; Michael Tyka; Steven M. Lewis; Oliver F. Lange; James Thompson; Ron Jacak; Kristian Kaufman; P. Douglas Renfrew; Colin A. Smith; Will Sheffler; Ian W. Davis; Seth Cooper; Adrien Treuille; Daniel J. Mandell; Florian Richter; Yih En Andrew Ban; Sarel J. Fleishman; Jacob E. Corn; David E. Kim; Sergey Lyskov; Monica Berrondo; Stuart Mentzer; Zoran Popović; James J. Havranek; John Karanicolas; Rhiju Das; Jens Meiler; Tanja Kortemme; Jeffrey J. Gray; Brian Kuhlman; David Baker; Philip Bradley

doi:10.1016/B978-0-12-381270-4.00019-6

Rosetta3: An object-oriented software suite for the simulation and design of macromolecules

Andrew Leaver-Fay, Michael Tyka, Steven M. Lewis, Oliver F. Lange, James Thompson, Ron Jacak, Kristian Kaufman, P. Douglas Renfrew, Colin A. Smith, Will Sheffler, Ian W. Davis, Seth Cooper, Adrien Treuille, Daniel J. Mandell, Florian Richter, Yih En Andrew Ban, Sarel J. Fleishman, Jacob E. Corn, David E. Kim, Sergey LyskovMonica Berrondo, Stuart Mentzer, Zoran Popović, James J. Havranek, John Karanicolas, Rhiju Das, Jens Meiler, Tanja Kortemme, Jeffrey J. Gray, Brian Kuhlman, David Baker, Philip Bradley

Cancer Signaling and Microenvironment (CSM)

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

1538 Scopus citations

Abstract

We have recently completed a full rearchitecturing of the Rosetta molecular modeling program, generalizing and expanding its existing functionality. The new architecture enables the rapid prototyping of novel protocols by providing easy-to-use interfaces to powerful tools for molecular modeling. The source code of this rearchitecturing has been released as Rosetta3 and is freely available for academic use. At the time of its release, it contained 470,000 lines of code. Counting currently unpublished protocols at the time of this writing, the source includes 1,285,000 lines. Its rapid growth is a testament to its ease of use. This chapter describes the requirements for our new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform.

Original language	English
Title of host publication	Methods in Enzymology
Publisher	Academic Press Inc.
Pages	545-574
Number of pages	30
Volume	487
Edition	C
DOIs	https://doi.org/10.1016/B978-0-12-381270-4.00019-6
State	Published - 2011

Publication series

Name	Methods in enzymology
ISSN (Print)	0076-6879

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Leaver-Fay, A., Tyka, M., Lewis, S. M., Lange, O. F., Thompson, J., Jacak, R., Kaufman, K., Renfrew, P. D., Smith, C. A., Sheffler, W., Davis, I. W., Cooper, S., Treuille, A., Mandell, D. J., Richter, F., Ban, Y. E. A., Fleishman, S. J., Corn, J. E., Kim, D. E., ... Bradley, P. (2011). Rosetta3: An object-oriented software suite for the simulation and design of macromolecules. In Methods in Enzymology (C ed., Vol. 487, pp. 545-574). (Methods in enzymology). Academic Press Inc.. https://doi.org/10.1016/B978-0-12-381270-4.00019-6

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title = "Rosetta3: An object-oriented software suite for the simulation and design of macromolecules",

abstract = "We have recently completed a full rearchitecturing of the Rosetta molecular modeling program, generalizing and expanding its existing functionality. The new architecture enables the rapid prototyping of novel protocols by providing easy-to-use interfaces to powerful tools for molecular modeling. The source code of this rearchitecturing has been released as Rosetta3 and is freely available for academic use. At the time of its release, it contained 470,000 lines of code. Counting currently unpublished protocols at the time of this writing, the source includes 1,285,000 lines. Its rapid growth is a testament to its ease of use. This chapter describes the requirements for our new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform.",

author = "Andrew Leaver-Fay and Michael Tyka and Lewis, {Steven M.} and Lange, {Oliver F.} and James Thompson and Ron Jacak and Kristian Kaufman and Renfrew, {P. Douglas} and Smith, {Colin A.} and Will Sheffler and Davis, {Ian W.} and Seth Cooper and Adrien Treuille and Mandell, {Daniel J.} and Florian Richter and Ban, {Yih En Andrew} and Fleishman, {Sarel J.} and Corn, {Jacob E.} and Kim, {David E.} and Sergey Lyskov and Monica Berrondo and Stuart Mentzer and Zoran Popovi{\'c} and Havranek, {James J.} and John Karanicolas and Rhiju Das and Jens Meiler and Tanja Kortemme and Gray, {Jeffrey J.} and Brian Kuhlman and David Baker and Philip Bradley",

year = "2011",

doi = "10.1016/B978-0-12-381270-4.00019-6",

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volume = "487",

series = "Methods in enzymology",

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Leaver-Fay, A, Tyka, M, Lewis, SM, Lange, OF, Thompson, J, Jacak, R, Kaufman, K, Renfrew, PD, Smith, CA, Sheffler, W, Davis, IW, Cooper, S, Treuille, A, Mandell, DJ, Richter, F, Ban, YEA, Fleishman, SJ, Corn, JE, Kim, DE, Lyskov, S, Berrondo, M, Mentzer, S, Popović, Z, Havranek, JJ, Karanicolas, J, Das, R, Meiler, J, Kortemme, T, Gray, JJ, Kuhlman, B, Baker, D & Bradley, P 2011, Rosetta3: An object-oriented software suite for the simulation and design of macromolecules. in Methods in Enzymology. C edn, vol. 487, Methods in enzymology, Academic Press Inc., pp. 545-574. https://doi.org/10.1016/B978-0-12-381270-4.00019-6

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T2 - An object-oriented software suite for the simulation and design of macromolecules

AU - Leaver-Fay, Andrew

AU - Tyka, Michael

AU - Lewis, Steven M.

AU - Lange, Oliver F.

AU - Thompson, James

AU - Jacak, Ron

AU - Kaufman, Kristian

AU - Renfrew, P. Douglas

AU - Smith, Colin A.

AU - Sheffler, Will

AU - Davis, Ian W.

AU - Cooper, Seth

AU - Treuille, Adrien

AU - Mandell, Daniel J.

AU - Richter, Florian

AU - Ban, Yih En Andrew

AU - Fleishman, Sarel J.

AU - Corn, Jacob E.

AU - Kim, David E.

AU - Lyskov, Sergey

AU - Berrondo, Monica

AU - Mentzer, Stuart

AU - Popović, Zoran

AU - Havranek, James J.

AU - Karanicolas, John

AU - Das, Rhiju

AU - Meiler, Jens

AU - Kortemme, Tanja

AU - Gray, Jeffrey J.

AU - Kuhlman, Brian

AU - Baker, David

AU - Bradley, Philip

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AB - We have recently completed a full rearchitecturing of the Rosetta molecular modeling program, generalizing and expanding its existing functionality. The new architecture enables the rapid prototyping of novel protocols by providing easy-to-use interfaces to powerful tools for molecular modeling. The source code of this rearchitecturing has been released as Rosetta3 and is freely available for academic use. At the time of its release, it contained 470,000 lines of code. Counting currently unpublished protocols at the time of this writing, the source includes 1,285,000 lines. Its rapid growth is a testament to its ease of use. This chapter describes the requirements for our new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform.

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BT - Methods in Enzymology

PB - Academic Press Inc.

ER -

Rosetta3: An object-oriented software suite for the simulation and design of macromolecules

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