GPU-Accelerated Generation of the Molecular Surface

Abstract

A variety of visualisation methods have been developed for displaying molecular structures. The solvent-excluded surface (SES) or molecular surface is one of the most popular and useful depictions as it helps to identify binding-site cavities. The molecular surface is particularly useful therefore for interactive molecular docking tools. Docking tools that incorporate molecular flexibility bring new challenges as the molecular surface must be recomputed in real time as the molecule changes shape in interaction with a ligand. Here we compute the SES by using a GPU-accelerated Marching Cubes algorithm which promises to lead to real-time surface generation for small- to medium-sized biomolecules undergoing conformational change.