New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations

✍ Scribed by Michael S. Lee; Michael Feig; Freddie R. Salsbury Jr.; Charles L. Brooks III

• Publisher: John Wiley and Sons
• Year: 2003
• Tongue: English
• Weight: 153 KB
• Volume: 24
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.10272

✦ Synopsis

Abstract

In a recent article (Lee, M. S.; Salsbury, F. R. Jr.; Brooks, C. L., III. J Chem Phys 2002, 116, 10606), we demonstrated that generalized Born (GB) theory provides a good approximation to Poisson electrostatic solvation energy calculations if one uses the same definitions of molecular volume for each. In this work, we present a new and improved analytic method for reproducing the Lee–Richards molecular volume, which is the most common volume definition for Poisson calculations. Overall, 1% errors are achieved for absolute solvation energies of a large set of proteins and relative solvation energies of protein conformations. We also introduce an accurate SASA approximation that uses the same machinery employed by our GB method and requires a small addition of computational cost. The combined methodology is shown to yield an efficient and accurate implicit solvent representation for simulations of biopolymers. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1348–1356, 2003