Calculation of Atomic Volume in Protein using Voronoi Diagram of Atoms

Abstract

The atomic volume, which is defined as the volume of Voronoi region of the atom, plays an important role for analysis of protein structures such as protein packing density, protein recognition and drug design. To precisely calculate the atomic volume, it is important to consider the atomic radius which is different for each atom type. The Voronoi diagram of atoms conveniently reflects the size difference precisely, not like the previous methods such as Voronoi diagram of point set and power diagram. In this study, the volume of individual atoms and?residues in protein are calculated via Voronoi diagram of atoms from a number of proteins already known their 3D structure.