Recognition of docking sites on a protein using beta-shape based on Voronoi diagram of atoms

Abstract

A protein consists of atoms. Given a protein, the automatic recognition of depressed regions on the surface of the protein, often called docking sites or pockets, is important for the analysis of interaction between a protein and a ligand and facilitates fast development of new drugs. Presented in this paper is a geometric approach for the detection of docking sites using beta-shape which is based on the Voronoi diagram for atoms in Euclidean distance metric. We first propose a geometric construct called a beta-shape which represents the proximity among atoms on the surface of a protein. Then, using the beta-shape, which takes the size differences among different atoms into account, we present an algorithm to extract the pockets for the possible docking site on the surface of a protein.