Accelerating the computation of triangulated molecular surfaces with OpenMP

Abstract

The ability to compute mesh representations of molecular surfaces in an accurate and timely manner is of great importance for applications such as implicit solvent modelling. The efficient computation of high-resolution mesh surfaces for large biomolecules is still a challenging task. This paper presents a fast, OpenMP-based parallel algorithm for the computation of the triangle mesh representation of the solvent-excluded surfaces of macromolecules at high resolutions. The solvent-excluded surface computation is based on a region-growing implementation of the approximate Euclidean distance transform algorithm with hierarchical queues. The method first builds a voxelised representation of the molecular surface by computing the contribution to the overall outer surface for each atom in parallel. Then, a triangle mesh representation is obtained from the voxelised one with an OpenMP-accelerated Marching Cubes implementation. The proposed algorithm was experimentally validated and was shown to outperform several state-of-the-art molecular surface computation tools on a dataset of large macromolecules.