A fast pairwise evaluation of molecular surface area
- PMID: 11948592
- DOI: 10.1002/jcc.10035
A fast pairwise evaluation of molecular surface area
Abstract
A fast and general analytical approach was developed for the calculation of the approximate van der Waals and solvent-accessible surface areas. The method is based on three basic ideas: the use of the Lorentz transformation formula, a rigid-geometry approximation, and a single fitting parameter that can be refitted on the fly during a simulation. The Lorentz transformation equation is used for the summation of the areas of an atom buried by its neighboring contacting atoms, and implies that a sum of the buried pairwise areas cannot be larger than the surface area of the isolated spherical atom itself. In a rigid-geometry approximation we numerically calculate and keep constant the surface of each atom buried by the atoms involved in 1-2 and 1-3 interactions. Only the contributions from the nonbonded atoms (1-4 and higher interactions) are considered in terms of the pairwise approximation. The accuracy and speed of the method is competitive with other pairwise algorithms. A major strength of the method is the ease of parametrization.
Copyright 2002 Wiley Periodicals, Inc.
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