Effective Atom Volumes for Implicit Solvent Models: Comparison between Voronoi Volumes and Minimum Fluctuation Volumes

摘要

An essential element of implicit solvent models, such as the generalized Born method, is a knowledge of the volume associated with the individual atoms of the solute. Two approaches for determining atomic atomic volumes for the generalized Born model are described; one is based on Voronoi polyhedra and the other, on minimizing the fluctuations in the overall volume of the solute. Volumes to be sued with various parameter sets for protein and nucleic acids in the CHARMM force field are determined from a large set of known structures. The volumes resulting from the two different approaches are compared with respect to various parameters, including the size an solvent accessibility of the structures from which they are determined., the question of whether to include hydroges in the atomic representation of the solute volume is examined