Visualization and analysis of protein structures using Euclidean Voronoi diagram of atoms

Abstract

Protein consists of amino acids, and an amino acid consists of atoms. Given a protein, understanding its functions is critical for various reasons for designing new drugs, treating diseases, and so on. Due to recent researches, it is now known that the structure of protein directly influences its functions. Hence, there have been strong research trends towards understanding the geometric structure of proteins. In this paper, we present a Euclidean Voronoi diagram of atoms constituting a protein and show how this computational tool can effectively and efficiently contribute to various important problems in biology. Some examples, among others, are the computations for molecular surface, solvent accessible surface, extraction of pockets, interaction interface, convex hull, etc.