Epock: rapid analysis of protein pocket dynamics | Zendy

Benoist Laurent | Zendy; Matthieu Chavent | Zendy; Tristan Cragnolini | Zendy; Anna Caroline E. Dahl | Zendy; Samuela Pasquali | Zendy; Philippe Derreumaux | Zendy; Mark S.P. Sansom | Zendy; Marc Baaden | Zendy

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Epock: rapid analysis of protein pocket dynamics

Author(s) -

Benoist Laurent,

Matthieu Chavent,

Tristan Cragnolini,

Anna Caroline E. Dahl,

Samuela Pasquali,

Philippe Derreumaux,

Mark S.P. Sansom,

Marc Baaden

Publication year - 2014

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btu822

Subject(s) - python (programming language) , plug in , computer science , scripting language , documentation , graphical user interface , programming language , interface (matter) , source code , operating system , bubble , maximum bubble pressure method

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.

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