title: MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories.
abstract: BACKGROUND
  A variety of pocket detection algorithms are now freely or commercially available to the scientific community for the analysis of static protein structures. However, since proteins are dynamic entities, enhancing the capabilities of these programs for the straightforward detection and characterization of cavities taking into account protein conformational ensembles should be valuable for capturing the plasticity of pockets, and therefore allow gaining insight into structure-function relationships.
  
  
  RESULTS
  This article describes a new method, called MDpocket, providing a fast, free and open-source tool for tracking small molecule binding sites and gas migration pathways on molecular dynamics (MDs) trajectories or other conformational ensembles. MDpocket is based on the fpocket cavity detection algorithm and a valuable contribution to existing analysis tools. The capabilities of MDpocket are illustrated for three relevant cases: (i) the detection of transient subpockets using an ensemble of crystal structures of HSP90; (ii) the detection of known xenon binding sites and migration pathways in myoglobin; and (iii) the identification of suitable pockets for molecular docking in P38 Map kinase.
  
  
  BACKGROUND
  MDpocket is free and open-source software and can be downloaded at http://fpocket.sourceforge.net.
  
  
  BACKGROUND
  pschmidtke@ub.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Departament de Fisicoquímica and Institut de Biomedicina, Universitat de Barcelona, 08028 Barcelona, Spain. pschmidtke@ub.edu
authors.forename: Peter
authors.initials: P
authors.lastname: Schmidtke
authors.forename: Axel
authors.initials: A
authors.lastname: Bidon-Chanal
authors.forename: F Javier
authors.initials: FJ
authors.lastname: Luque
authors.forename: Xavier
authors.initials: X
authors.lastname: Barril
mesh_terms: D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D019295:Computational Biology; D018841:HSP90 Heat-Shock Proteins / Q000737:chemistry; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D012984:Software; D048051:p38 Mitogen-Activated Protein Kinases / Q000737:chemistry
chemical_list: D018841:HSP90 Heat-Shock Proteins; D011506:Proteins; D048051:p38 Mitogen-Activated Protein Kinases