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Bioinformatics. 2011 Jun 1;27(11):1575-7. doi: 10.1093/bioinformatics/btr168. Epub 2011 Apr 5.

ProDy: protein dynamics inferred from theory and experiments.

Author information

1
Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA. ahb12@pitt.edu

Abstract

SUMMARY:

We developed a Python package, ProDy, for structure-based analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations in heterogeneous datasets of structures experimentally resolved for a given biomolecular system, and for comparison of these variations with the theoretically predicted equilibrium dynamics. Datasets include structural ensembles for a given family or subfamily of proteins, their mutants and sequence homologues, in the presence/absence of their substrates, ligands or inhibitors. Numerous helper functions enable comparative analysis of experimental and theoretical data, and visualization of the principal changes in conformations that are accessible in different functional states. ProDy application programming interface (API) has been designed so that users can easily extend the software and implement new methods.

AVAILABILITY:

ProDy is open source and freely available under GNU General Public License from http://www.csb.pitt.edu/ProDy/.

PMID:
21471012
PMCID:
PMC3102222
DOI:
10.1093/bioinformatics/btr168
[Indexed for MEDLINE]
Free PMC Article

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