Finding surface atoms of a protein molecule on a GPU

Abstract

We present a real-time method to find the atoms at the boundary surface of a protein molecule. Efficient finding of the atoms at the surface of the molecule is important since most of interactions between two protein molecules including docking and binding occur at the boundary surface of molecules. [Deanda, et al. 2002] proposed a method to extract surface atoms based on solvent-accessible surfaces. Solvent-accessible surface is a trajectory of the center of probe solvent, where the solvent touches the molecule without interference. They defined surface atoms as the atoms that touch the solvent probes. We represent the protein molecule as a set of spheres with van der Waals radii: M = {S(c i, r i)}, where S(c i, r i) is a sphere with center point c i and radius r i. The probe solvent is represented as a sphere with radius d. We compute the offset surface of M with offset distance d. Then, we find the spheres in M, whose d-offset surface has an intersection with the d-offset surface of M. To achieve the real-time performance, our algorithm is implemented on a GPU.