Virginio Cantoni, Riccardo Gatti, Luca Lombardi

Keywords: Structural biology, protein structure analysis, protein-ligand interaction, surface segmentation.

Abstract: The study of the 3D structure of proteins supports the investigation of their functions and represents an initial step towards protein based drug design. The goal of this paper is to define a technique, based on the geometrical and topological structure of protein surfaces, for the detection and the analysis of sites of possible protein-protein and protein-ligand interactions. In particular, the aims is to identify concave and convex regions which constitute ‘pockets’ and ‘protuberance’ that can make up the interactions ‘active sites’. A segmentation process is applied to the solvent-excluded-surface (SES) through a sequence of propagation steps applied to the region between the protein convex-hull and the SES: the first phase generates the pockets (and tunnels) set, meanwhile the second (backwards) produces the protrusions set.