An Efficient Method for Sampling and Computing Molecular Surface

An atom-centered protocol based method for surface sampling in grid space is proposed. Van der Waals, solvent-accessible and solvent-excluded surface can be generated in a unified framework. A spherical hash function is used to mark whether the points are inside a sphere, and the hash tables are used to record which spheres the surface points locate on. The proposed method can be modified to apply in the parallel computation directly, which is useful for molecular dynamics simulation, docking and surface comparison and so on. Our tests indicate that the proposed method is efficient and the generated surfaces are suitable for quantitative analysis and visualization.