Rosettascripts: A scripting language interface to the Rosetta Macromolecular modeling suite

Sarel J. Fleishman, Andrew Leaver-Fay, Jacob E. Corn, Eva Maria Strauch, Sagar D. Khare, Nobuyasu Koga, Justin Ashworth, Paul Murphy, Florian Richter, Gordon Lemmon, Jens Meiler, David Baker

Research output: Contribution to journalArticlepeer-review

224 Scopus citations

Abstract

Macromolecular modeling and design are increasingly useful in basic research, biotechnology, and teaching. However, the absence of a user-friendly modeling framework that provides access to a wide range of modeling capabilities is hampering the wider adoption of computational methods by non-experts. RosettaScripts is an XML-like language for specifying modeling tasks in the Rosetta framework. RosettaScripts provides access to protocol-level functionalities, such as rigid-body docking and sequence redesign, and allows fast testing and deployment of complex protocols without need for modifying or recompiling the underlying C++ code. We illustrate these capabilities with RosettaScripts protocols for the stabilization of proteins, the generation of computationally constrained libraries for experimental selection of higher-affinity binding proteins, loop remodeling, small-molecule ligand docking, design of ligand-binding proteins, and specificity redesign in DNA-binding proteins.

Original languageEnglish (US)
Article numbere20161
JournalPloS one
Volume6
Issue number6
DOIs
StatePublished - 2011
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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