Joint neighbors approximation of macromolecular solvent accessible surface area

Abstract

A new method for approximate analytical calculations of solvent accessible surface area (SASA) for arbitrary molecules and their gradients with respect to their atomic coordinates was developed. This method is based on the recursive procedure of pairwise joining of neighboring atoms. Unlike other available methods of approximate SASA calculations, the method has no empirical parameters, and therefore can be used with comparable accuracy in calculations of SASA in folded and unfolded conformations of macromolecules of any chemical nature. As shown by tests with globular proteins in folded conformations, average errors in absolute atomic surface area is around 1 Ų, while for unfolded protein conformations it varies from 1.65 to 1.87 Ų. Computational times of the method are comparable with those by GETAREA, one of the fastest exact analytical methods available today. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007