Epock: rapid analysis of protein pocket dynamics

Abstract

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.

Fig. 1.

(A) Graphical interface of Epock’s VMD plugin for defining the MER using a combination of sphere volumes to include (central sphere) and exclude (surrounding spheres), resulting in a fine-tunable geometric shape for analysis. (B) Grid points composing the MER. (C) Pocket volume (marked by two arrows) and residue contribution (second curve) of Y197 during an MD simulation. (D) Standard deviations of residue contribution ordered from highest to lowest. (E, F) Protein conformation (surface in mesh, backbone as tube) and pocket (Y197 as spheres coloured by atom type, pocket accessible space as joint spheres) at t = 1500 ps (E) and t = 3500 ps (F)