A Visual Analytics of Geometric Distances between Amino Acids and Surface Pockets of Proteins

Abstract

Abstract-Protein is the major component of the organism. It has a unique three-dimensional structure formed by its amino acid sequence. A concave (pocket) on the surface of a protein is known to be the best target for a drug to react. We started analyzing how "druggability" of proteins related to the location of amino acids in a pocket. This paper presents a visualization tool for distance analysis between pockets and the amino acid residue. Provided that a protein surface is described by a triangular mesh, this tool first identifies pockets on the protein surface, specifies the deepest point and outer loops of the pocket, and calculates distances between atoms of an amino acid residue and the deepest point or the outer loops of the pocket. The tool then visualizes the statistics of the distance calculation results by polyline charts and the distribution by scatterplots. This paper proposes a biological interpretation of the visualization results.