title: Epock: rapid analysis of protein pocket dynamics.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  Epock C++ source code, Python analysis scripts, VMD Tcl plugin, documentation and installation instructions are freely available at http://epock.bitbucket.org.
  
  
  BACKGROUND
  benoist.laurent@gmail.com or baaden@smplinux.de
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
authors.forename: Benoist
authors.initials: B
authors.lastname: Laurent
authors.affiliation: Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Chavent
authors.affiliation: Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
authors.forename: Tristan
authors.initials: T
authors.lastname: Cragnolini
authors.affiliation: Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
authors.forename: Anna Caroline E
authors.initials: AC
authors.lastname: Dahl
authors.affiliation: Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
authors.forename: Samuela
authors.initials: S
authors.lastname: Pasquali
authors.affiliation: Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
authors.forename: Philippe
authors.initials: P
authors.lastname: Derreumaux
authors.affiliation: Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
authors.forename: Mark S P
authors.initials: MS
authors.lastname: Sansom
authors.affiliation: Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
authors.forename: Marc
authors.initials: M
authors.lastname: Baaden
mesh_terms: D001665:Binding Sites; D018841:HSP90 Heat-Shock Proteins / Q000737:chemistry / Q000378:metabolism; D007473:Ion Channels / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation; D012984:Software
chemical_list: D018841:HSP90 Heat-Shock Proteins; D007473:Ion Channels