A RAPID METHOD FOR CALCULATING DERIVATIVES OF SOLVENT ACCESSIBLE SURFACE-AREAS OF MOLECULES

A novel method to calculate the derivatives of solvent accessible surf ace areas is presented. Unlike earlier analytic methods, which require the molecular topology and the use of global Gauss-Bonnet theorem, th is method requires only the fractional accessibilities of surface arcs . We developed an efficient numerical algorithm to calculate the surfa ce arcs by creating a uniform set of points on the circles of intersec tion between surface atoms. A hierarchical point density doubling sche me led to a logarithmic dependence of Central Processing Unit (CPU) ti me on the number of points used. This algorithm calculated area deriva tives for a 1000-atom protein in 1.5 s on an SGI INDIGO(2) which were within 2% of the analytic area derivatives calculated with the program ANAREA. This algorithm scales Linearly with the number of atoms for l arge molecules and is easily parallelizable. (C) 1995 by John Wiley & Sons, Inc.