Getting poster data...
Daria B. Kokh, Stefan Henrich, Paul Czodrowski, Friedrich Rippmann, Rebecca C. Wade (Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany)In rational drug design, complementarity of a protein cavity and a ligand is one of the most important factors for binding and usually a prerequisite in searches for potential therapeutic agents. Binding pockets in proteins are not, however, static entities. Their shape may vary considerably due to protein flexibility, leading to alteration of their physical properties and, therefore, of the apparent druggability of the binding site relative to that of an experimentally determined structure. Knowledge of binding site dynamics may open up new perspectives for the design of compounds with steric or other properties differing from those of known binders. We will 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. TRAPP performs accurate grid-based calculations of the shape and physicochemical characteristics of a binding pocket for each structure, detects transient regions of the pocket, and prepare a set of scripts for visualization of the pocket dynamics and properties using Pymol, JMol, or Chimera.