QuickSES: A Library for Fast Computation of Solvent Excluded Surfaces

Abstract

Recently, several fast methods to compute Solvent Excluded Surfaces (SES) on GPUs have been presented. While these published methods reportedly yield interesting and useful results, up to now no public, freely accessible implementation of a fast and opensource SES mesh computation method that runs on GPUs is available. Most molecular viewers, therefore, still use legacy CPU methods that run only on a single core, without GPU acceleration. In this paper, we present an in-depth explanation and a fully open-source CUDA implementation of the fast, grid-based computation method proposed by Hermosilla et al. [HKG*17]. Our library called QuickSES runs on GPUs and is distributed with a permissive license. It comes with a standalone program that reads Protein Data Bank (PDB) files and outputs a complete SES mesh as a Wavefront OBJ file. Alternatively it can directly be integrated in classical molecular viewers as shared library. We demonstrate the low memory consumption to enable execution on lower-end GPUs, and compare the runtime speed-up to available state-of-the-art tools.