A New Program to Compute the Surface Properties of Biomolecules

The interactions of large molecules with surfaces and with each other are strongly dependent upon their surface, rather than their bulk properties. In addition, the local properties of biomolecular surfaces are very important in their own right in biomedicine and other areas, for example for locating binding sites. Following to previous work, we have developed a program to compute to compute amino acid and atom-based surface descriptors, and used it to generate a small database of charge and hydrophobicity-related surface properties for a set of proteins. The program requires the user to input two text files: one assigning a real number to each atom of each amino acid, and one assigning a real number to each amino acid. Although we have so far only computed surface charge (atom-based) and surface hydrophobicity (amino acid-based), we note that this program could be used to compute any surface parameter whatsoever, since the user can assign arbitrary atom-by-atom and amino acid properties. We discuss possible applications of this program and describe one current application, the Biomolecular Adsorption Database.