TRAPP on the Frontpage

An article by HITS researcher Dr. Daria Kokh (MCM) has made it onto the frontpage of the Journal of Chemical Information and Modeling. TRAPP (A Tool for Analysis of Transient Binding Pockets in Proteins) is 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. These variations 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. It detects the conserved and transient regions of the pocket in an ensemble of protein conformations. The platform 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. The project was conducted in cooperation with Merck-Serono, Darmstadt. D. B. Kokh, S. Richter, S. Henrich, P. Czodrowski, F. Rippmann, and R. C. Wade, J. Chem. Inf. Model., 2013, 53 (5), pp 1235–1252.