A List-Based Method for Fast Generation of Molecular Surfaces

In this paper we present a fast and reliable method for generation of molecular surfaces. While the method is readily applicable to van der Waals surface generation, we shall be focusing on solvent-accessible surfaces (SAS) and solvent-excluded surfaces (SES) of a molecule. A list-based method is utilized to represent and generate the union of multiple spheres with arbitrary radii, with which we are able to produce the SAS and SES of a molecule in a very efficient way. The surface generated is represented by a quadrilateral mesh, which can be easily converted into a triangular mesh if needed. Some results will be provided to demonstrate the speed and quality of our mesh generation algorithms.