title: TRAPP: a tool for analysis of transient binding pockets in proteins.
abstract: We present TRAPP (TRAnsient Pockets in Proteins), a new automated software platform for tracking, analysis, and visualization of binding pocket variations along a protein motion trajectory or within an ensemble of protein structures that may encompass conformational changes ranging from local side chain fluctuations to global backbone motions. TRAPP performs accurate grid-based calculations of the shape and physicochemical characteristics of a binding pocket for each structure and detects the conserved and transient regions of the pocket in an ensemble of protein conformations. It also provides tools for tracing the opening of a particular subpocket and residues that contribute to the binding site. TRAPP thus enables an assessment of the druggability of a disease-related target protein taking its flexibility into account.
authors.affiliation: Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany. daria.kokh@h-its.org
authors.forename: Daria B
authors.initials: DB
authors.lastname: Kokh
authors.forename: Stefan
authors.initials: S
authors.lastname: Richter
authors.forename: Stefan
authors.initials: S
authors.lastname: Henrich
authors.forename: Paul
authors.initials: P
authors.lastname: Czodrowski
authors.forename: Friedrich
authors.initials: F
authors.lastname: Rippmann
authors.forename: Rebecca C
authors.initials: RC
authors.lastname: Wade
mesh_terms: D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D008024:Ligands; D056004:Molecular Dynamics Simulation; D025341:Principal Component Analysis; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins