Numerical calculation of molecular surface area. II. Speed of calculation

Abstract

A new fast and accurate algorithm for numerical calculation of the van der Waals and solvent accessible surface areas based on the sorted table of cosines is described. This algorithm does not depend upon the particular distribution of the points on the sphere surface, and thus allows use of the most accurate points distribution available. Direct comparisons (on the same computer) with other known fast algorithms are performed. The comparisons show that this algorithm is the fastest when accurate calculation of the van der Waals surface is required and is at least as fast as the fastest competitor algorithm for the evaluation of the solvent accessible surface area. Show more