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.
The Heidelberg Institute for Theoretical Studies (HITS) was established in 2010 by the physicist and SAP co-founder Klaus Tschira (1940-2015) and the Klaus Tschira Foundation as a private, non-profit research institute. HITS conducts basic research in the natural sciences, mathematics and computer science, with a focus on the processing, structuring, and analyzing of large amounts of complex data and the development of computational methods and software. The research fields range from molecular biology to astrophysics. The shareholders of HITS are the HITS-Stiftung, which is a subsidiary of the Klaus Tschira Foundation, Heidelberg University and the Karlsruhe Institute of Technology (KIT). HITS also cooperates with other universities and research institutes and with industrial partners. The base funding of HITS is provided by the HITS Stiftung with funds received from the Klaus Tschira Foundation. The primary external funding agencies are the Federal Ministry of Education and Research (BMBF), the German Research Foundation (DFG), and the European Union.