MDpocket : Open Source Cavity Detection and Characterization on Molecular Dynamics Trajectories

TitleMDpocket : Open Source Cavity Detection and Characterization on Molecular Dynamics Trajectories
Publication TypeJournal Article
Year of Publication2011
AuthorsSchmidtke, P, Bidon-Chanal A, Luque FJ, Barril X
JournalBioinformatics (Oxford, England)
Date Published2011/10/03/
AbstractMOTIVATION: 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 paper 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 MD 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 sub-pockets 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. AVAILABILITY: MDpocket is free and open source software and can be downloaded at CONTACT: SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.