期刊
JOURNAL OF COMPUTATIONAL CHEMISTRY
卷 27, 期 1, 页码 72-89出版社
WILEY
DOI: 10.1002/jcc.20307
关键词
Born model; novel Gaussian surface; biomolecules; implicit solvent model; solvation energy; protein structure prediction; loop structure prediction; energy minimization; molecular surface
资金
- NIGMS NIH HHS [R01 GM052018, GM56531, GM-52018, P01 GM071790, R01 GM052018-12, GM071790, P01 GM056531] Funding Source: Medline
We have developed a version of our surface generalized Born (SGB) model that employs a Gaussian surface, as opposed to the van der Waals surface used previously. The Gaussian surface is smooth and its properties are analytically differentiable with respect to the positions of atoms. A significant advantage of a solvent model based on this analytically differentiable surface is the availability of analytical gradients of the surface and solvation forces. An efficient and robust algorithm is designed to construct and triangulate the Gaussian surface for large biomolecules with arbitrary shapes, and to compute the various terms required for energy gradients. The Gaussian surface is shown to better mimic the boundary between the solute and solvent by properly addressing solvent accessibility, as is demonstrated by comparisons with standard Poisson-Boltzmann calculations for proteins of different sizes. These results also demonstrate that surface definition is a dominant contribution to differences between GB and PB calculations, especially if the system is large. Application of the new surface to prediction of long loop regions is presented, and significant improvement in the energetics is seen compared with results obtained using the van der Waals surface, even in the absence of optimized empirical correction terms that were used in the latter calculations.
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