On-the-fly Numerical Surface Integration for Finite-Difference Poisson-Boltzmann Methods.
Most implicit solvation models require the definition of a molecular surface as the interface that separates the solute in atomic detail from the solvent approximated as a continuous medium. Commonly used surface definitions include the solvent accessible surface (SAS), the solvent excluded surface (SES), and the van der Waals surface. In this study, we present an efficient numerical algorithm to compute the SES and SAS areas to facilitate the applications of finite-difference Poisson-Boltzmann methods in biomolecular simulations. Different from previous numerical approaches, our algorithm is physics-inspired and intimately coupled to the finite-difference Poisson-Boltzmann methods to fully take advantage of its existing data structures. Our analysis shows that the algorithm can achieve very good agreement with the analytical method in the calculation of the SES and SAS areas. Specifically, in our comprehensive test of 1,555 molecules, the average unsigned relative error is 0.27% in the SES area calculations and 1.05% in the SAS area calculations at the grid spacing of 1/2Å. In addition, a systematic correction analysis can be used to improve the accuracy for the coarse-grid SES area calculations, with the average unsigned relative error in the SES areas reduced to 0.13%. These validation studies indicate that the proposed algorithm can be applied to biomolecules over a broad range of sizes and structures. Finally, the numerical algorithm can also be adapted to evaluate the surface integral of either a vector field or a scalar field defined on the molecular surface for additional solvation energetics and force calculations.
Department of Biomedical Engineering, University of California, Irvine, California ; Department of Molecular Biology and Biochemistry, University of California, Irvine, California.
Qin
Q
Cai
Department of Molecular Biology and Biochemistry, University of California, Irvine, California ; Department of Physics, Shanghai Normal University, Shanghai, China.
Xiang
X
Ye
Department of Molecular Biology and Biochemistry, University of California, Irvine, California.
Jun
J
Wang
Department of Biomedical Engineering, University of California, Irvine, California ; Department of Molecular Biology and Biochemistry, University of California, Irvine, California.
Ray
R
Luo