A revised density function for molecular surface definition in continuum solvent models.

ABSTRACT: A revised density function is developed to define the molecular surface for the numerical Poisson-Boltzmann methods to achieve a better convergence and higher numerical stability. The new density function does not use any predefined functional form but is numerically optimized to reproduce the reaction field energies computed with the solvent excluded surface definition. An exhaustive search in the parameter space is utilized in the optimization using a wide-range training molecules including proteins, nucleic acids, and peptides in both folded and unfolded conformations. A cubic-spline function is introduced to guarantee good numerical behavior of the new density function. Our test results show that the average relative energy errors computed with the revised density function are uniforml

SUBMITTER: Ye X 

PROVIDER: S-EPMC3979486 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature