title: A novel approach for identifying the surface atoms of macromolecules.
abstract: 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.
authors.affiliation: Laboratory for the Development of Computer-Assisted Drug Discovery Software, College of Pharmacy, University of Texas, Austin 78712, USA. fd69145@glaxowellcome.com
authors.forename: Felix
authors.initials: F
authors.lastname: Deanda
authors.forename: Robert S
authors.initials: RS
authors.lastname: Pearlman
mesh_terms: D003196:Computer Graphics; D003198:Computer Simulation; D017076:Computer-Aided Design; D046911:Macromolecular Substances; D011506:Proteins / Q000737:chemistry*; D012997:Solvents; D055672:Static Electricity; D013499:Surface Properties
chemical_list: D046911:Macromolecular Substances; D011506:Proteins; D012997:Solvents