A rapid method for calculating derivatives of solvent accessible surface areas of molecules

A novel method to calculate the derivatives of solvent accessible surface areas is presented. Unlike earlier analytic methods, which require the molecular topology and the use of global Gauss‐Bonnet theorem, this method requires only the fractional accessibilities of surface arcs. We developed an efficient numerical algorithm to calculate the surface arcs by creating a uniform set of points on the circles of intersection between surface atoms. A hierarchical point density doubling scheme led to a logarithmic dependence of Central Processing Unit (CPU) time on the number of points used. This algorithm calculated area derivatives for a 1000‐atom protein in 1.5 s on an SGI INDIGO2 which were within 2% of the analytic area derivatives calculated with the program ANAREA. This algorithm scales linearly with the number of atoms for large molecules and is easily parallelizable.