Abstract: System that generates the solvent-excluded surface (SES) of a molecule using a parallel algorithm that may execute on a GPU. Parallel execution allows a SES to be created in seconds even for a large protein, or to be recreated rapidly when exploring modifications to molecular structure. The algorithm calculates a spatial field that represents a signed distance between an atom-facing surface of a probe and each point in 3D grid. Spatial field calculations for different grid points may be performed in parallel. The SES is then obtained as the zero isosurface of the spatial field, using for example marching cubes. Atoms and probes may be placed into spatial buckets and indexed by bucket to improve efficiency by limiting calculations to atoms and probes in the proximity of a point.