A novel approach for identifying the surface atoms of macromolecules
A significant number of atoms lie buried beneath the molecular surface of proteins and other biologic macromolecules. Interactions between ligands and these macromolecules are dominated by interactions with the surface atoms. Although interactions with the buried or interior atoms of the macromolecule certainly contribute to the total intermolecular interaction energy, many computer-assisted drug design (CADD) strategies can benefit from the identification of those atoms on the surface of proteins and other macromolecules. We have developed a simple, yet novel method to distinguish the surface atoms of macromolecules from the interior atoms which is based on computing the atomic contributions to the solvent-accessible surface (SAS) area. This report describes that method and demonstrates that it compares very favorably with four alternative methods.
surface atoms interior atoms macromolecular surface solvent-accessible surface area