ROSETTA3: an Object-oriented Software Suite for the Simulation and Design of Macromolecules

Overview

Journal Methods Enzymol

Specialty Biochemistry

Date 2010 Dec 29

PMID 21187238

Citations 975

Authors

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 Popovic

James J Havranek

John Karanicolas

Rhiju Das

Jens Meiler

Tanja Kortemme

Jeffrey J Gray

Brian Kuhlman

David Baker

Philip Bradley

Affiliations

Soon will be listed here.

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 Counting currently unpublished protocols at the time of this writing, the source includes 1,285,000 lines.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.

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