title: ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.
abstract: We have recently completed a full re-architecturing 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 Counting currently unpublished protocols at the time of this writing, the source includes 1,285,000 lines.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.
authors.affiliation: Department of Biochemistry, University of North Carolina, Chapel Hill, North Carolina, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Leaver-Fay
authors.forename: Michael
authors.initials: M
authors.lastname: Tyka
authors.forename: Steven M
authors.initials: SM
authors.lastname: Lewis
authors.forename: Oliver F
authors.initials: OF
authors.lastname: Lange
authors.forename: James
authors.initials: J
authors.lastname: Thompson
authors.forename: Ron
authors.initials: R
authors.lastname: Jacak
authors.forename: Kristian
authors.initials: K
authors.lastname: Kaufman
authors.forename: P Douglas
authors.initials: PD
authors.lastname: Renfrew
authors.forename: Colin A
authors.initials: CA
authors.lastname: Smith
authors.forename: Will
authors.initials: W
authors.lastname: Sheffler
authors.forename: Ian W
authors.initials: IW
authors.lastname: Davis
authors.forename: Seth
authors.initials: S
authors.lastname: Cooper
authors.forename: Adrien
authors.initials: A
authors.lastname: Treuille
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Mandell
authors.forename: Florian
authors.initials: F
authors.lastname: Richter
authors.forename: Yih-En Andrew
authors.initials: YE
authors.lastname: Ban
authors.forename: Sarel J
authors.initials: SJ
authors.lastname: Fleishman
authors.forename: Jacob E
authors.initials: JE
authors.lastname: Corn
authors.forename: David E
authors.initials: DE
authors.lastname: Kim
authors.forename: Sergey
authors.initials: S
authors.lastname: Lyskov
authors.forename: Monica
authors.initials: M
authors.lastname: Berrondo
authors.forename: Stuart
authors.initials: S
authors.lastname: Mentzer
authors.forename: Zoran
authors.initials: Z
authors.lastname: Popović
authors.forename: James J
authors.initials: JJ
authors.lastname: Havranek
authors.forename: John
authors.initials: J
authors.lastname: Karanicolas
authors.forename: Rhiju
authors.initials: R
authors.lastname: Das
authors.forename: Jens
authors.initials: J
authors.lastname: Meiler
authors.forename: Tanja
authors.initials: T
authors.lastname: Kortemme
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Gray
authors.forename: Brian
authors.initials: B
authors.lastname: Kuhlman
authors.forename: David
authors.initials: D
authors.lastname: Baker
authors.forename: Philip
authors.initials: P
authors.lastname: Bradley
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D046911:Macromolecular Substances / Q000737:chemistry*; D008958:Models, Molecular; D012984:Software
chemical_list: D046911:Macromolecular Substances; D004247:DNA