Protein geometry: volumes, areas and distances

Abstract

In this chapter, methods for the calculation of the volumes and areas of proteins are surveyed. The application of Voronoi polyhedra to the calculation of volumes is focused on, with a discussion of how this construction is made and various aspects of it, including the calculation of standard sets of protein volumes. Various measures for protein surface areas, including the accessible surface area, are also discussed. Keywords: molecular surface; molecular volumes; surface areas; surface-area calculation; surfaces; Voronoi construction; Voronoi polyhedra