PyRosetta: A script-based interface for implementing molecular modeling algorithms using Rosetta

Sidhartha Chaudhury, Sergey Lyskov, Jeffrey J Gray

Research output: Contribution to journalArticle

Abstract

PyRosetta is a stand-alone Python-based imple-mentation of the Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using the major Rosetta sampling and scoring functions. PyRosetta contains Python bindings to libraries that define Rosetta functions including those for accessing and manipulating protein structure, calculating energies and running Monte Carlo-based simulations. PyRosetta can be used in two ways: (i) interactively, using iPython and (ii) script-based, using Python scripting. Interactive mode contains a number of help features and is ideal for beginners while script-mode is best suited for algorithm development. PyRosetta has similar computational performance to Rosetta, can be easily scaled up for cluster applications and has been implemented for algorithms demonstrating protein docking, protein folding, loop modeling and design. Availability: PyRosetta is a stand-alone package available at http://www.pyrosetta.org under the Rosetta license which is free for academic and non-profit users. A tutorial, user's manual and sample scripts demonstrating usage are also available on the web site. Contact: pyrosetta@graylab.jhu.edu

Original languageEnglish (US)
Article numberbtq007
Pages (from-to)689-691
Number of pages3
JournalBioinformatics
Volume26
Issue number5
DOIs
StatePublished - Jan 7 2010

Fingerprint

Boidae
Molecular Modeling
Python
Molecular modeling
Proteins
Protein folding
Structure Prediction
Protein Folding
Docking
Algorithm Design
Protein Structure
Licensure
Scoring
Running
Libraries
Websites
Availability
Contact
Sampling
Protein

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

PyRosetta : A script-based interface for implementing molecular modeling algorithms using Rosetta. / Chaudhury, Sidhartha; Lyskov, Sergey; Gray, Jeffrey J.

In: Bioinformatics, Vol. 26, No. 5, btq007, 07.01.2010, p. 689-691.

Research output: Contribution to journalArticle

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