This Small Business Innovation Research Phase I project will develop computational methods for dynamically recomputing the solvent-accessible molecular surface as the molecule changes its conformation. The solvent-accessible molecular surface has been defined by Fred Richards of Yale University to be a smooth envelope surrounding a protein molecule. It has been found to be useful in studying protein-protein and drug-protein binding. Current methods for computing this surface recompute the entire surface even if just some of the atoms move. Recomputing the surface for just the region that has changed would result in a great savings in computation time and would allow a user of an interactive molecular display system to alter the protein conformation and watch the surface be recomputed in near real time. Applications include (a) protein homology model building, (b) site-specific mutagenesis in protein engineering, and (c) crystallographic structural uncertainty, where there are several possible orientations of a surface amino acid side chain.
