A revised density function for molecular surface definition in continuum solvent models.
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 uniformly lower than 1% for both training and test molecules with different sizes and conformations. Our transferability analysis shows that the performance of the new method is mostly size and conformation independent. A detailed analysis further shows that the numerical forces computed with the revised density function converge better with respect to the grid spacing and are numerically more stable in tested peptides.
Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900.
Xiang
X
Ye
Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900.
Jun
J
Wang
Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900 ; Department of Biomedical Engineering, University of California, Irvine, California 92697-3900.
Ray
R
Luo