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SUMMARY: The volume of an internal protein pocket is fundamental to ligand accessibility. Few programs that compute such volumes manage dynamic data from molecular dynamics (MD) simulations. Limited performance often prohibits analysis of large datasets. We present Epock, an efficient command-line tool that calculates pocket volumes from MD trajectories. A plugin for the VMD program provides a graphical user interface to facilitate input creation, run Epock and analyse the results. AVAILABILITY AND IMPLEMENTATION: Epock C++ source code, Python analysis scripts, VMD Tcl plugin, documentation and installation instructions are freely available at http://epock.bitbucket.org. CONTACT: benoist.laurent@gmail.com or baaden@smplinux.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original publication

DOI

10.1093/bioinformatics/btu822

Type

Journal article

Journal

Bioinformatics

Publication Date

01/05/2015

Volume

31

Pages

1478 - 1480

Keywords

Binding Sites, HSP90 Heat-Shock Proteins, Ion Channels, Molecular Dynamics Simulation, Protein Binding, Protein Conformation, Software