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

J Comput Chem. 2003 Aug;24(11):1348-56. doi: 10.1002/jcc.10272.


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.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms*
  • Hydrogen Bonding
  • Models, Molecular*
  • Protein Conformation
  • Proteins / chemistry*
  • Solvents
  • Static Electricity
  • Thermodynamics


  • Proteins
  • Solvents