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RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite

Author

Listed:
  • 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

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.

Suggested Citation

  • 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, 2011. "RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite," PLOS ONE, Public Library of Science, vol. 6(6), pages 1-10, June.
    • Handle: RePEc:plo:pone00:0020161
    DOI: 10.1371/journal.pone.0020161
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    References listed on IDEAS

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    1. Summer B. Thyme & Jordan Jarjour & Ryo Takeuchi & James J. Havranek & Justin Ashworth & Andrew M. Scharenberg & Barry L. Stoddard & David Baker, 2009. "Exploitation of binding energy for catalysis and design," Nature, Nature, vol. 461(7268), pages 1300-1304, October.
    2. Justin Ashworth & James J. Havranek & Carlos M. Duarte & Django Sussman & Raymond J. Monnat & Barry L. Stoddard & David Baker, 2006. "Computational redesign of endonuclease DNA binding and cleavage specificity," Nature, Nature, vol. 441(7093), pages 656-659, June.
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