An accurate and robust algorithm for solvent-excluded surface computation

Abstract

The solvent-excluded surface (SES1) of a molecule is an important geometrical property relevant to its solvation in aqueous solution and its interactions with other molecules. In this paper we present an accurate and robust analytic algorithm suitable for a large-scale SES analysis. The accuracy and robustness of our algorithm are made possible by an iterative strategy for the treatments of probe-probe intersections, probe-probe overlaps and limited numerical precision. The accuracy and robustness of our algorithm in turn make it possible to analyze on a large-scale the SESs for different types of proteins and various sets of ligand-protein interaction interfaces. The results illustrate the usefulness of SES and SES-defined physical and geometrical properties for the characterization of protein-solvent interaction and ligand-protein interaction where ligand could be either small molecule compound, or membrane lipid, or DNA or protein.