Protein surfaces and volumes: measurement and use

Abstract

In the first part of 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. In the second part of the chapter, the calculation of molecular surface areas, the uses of surface-area calculations and the representation of molecular surfaces are discussed. Keywords: GRASP; atomic radii; binding energies; complete rolling algorithm; connected rolling algorithm; Connolly dot surface; convex hull; Delaunay triangulation; extended atoms; Gauss–Bonnet theorem; hydration surface; hydrophobicity; marching-cube algorithm; molecular packing; molecular surface; molecular volumes; packing efficiency; probe radius; probe sphere; representation of surfaces; solvent-accessible surface; surface areas; surface-area calculation; surfaces; vertex error; Voronoi construction; Voronoi polyhedra; van der Waals radii; van der Waals surface