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

Research output: Chapter in Book/Report/Conference proceedingChapter

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 Counting currently unpublished protocols at the time of this writing, the source includes 1,285,000 lines.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 languageEnglish (US)
Title of host publicationMethods in Enzymology
PublisherAcademic Press Inc.
Pages545-574
Number of pages30
EditionC
DOIs
StatePublished - 2011

Publication series

NameMethods in Enzymology
NumberC
Volume487
ISSN (Print)0076-6879

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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