New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.
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.
Lee
Michael S
MS
Department of Molecular Biology (TPC 6), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
Feig
Michael
M
Salsbury
Freddie R
FR
Brooks
Charles L
CL
D000465:Algorithms; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012997:Solvents; D055672:Static Electricity; D013816:Thermodynamics
D011506:Proteins; D012997:Solvents