期刊
JOURNAL OF COMPUTATIONAL CHEMISTRY
卷 35, 期 29, 页码 2132-2139出版社
WILEY
DOI: 10.1002/jcc.23728
关键词
Poisson-Boltzmann implicit solvent; implicit solvent; continuum electrostatics; solvation-free energy; molecular modeling
资金
- JSPS [236408]
- Protein 3000 Project of the Ministry of Education, Culture, Sports, Science, and Technology of Japan
The Poisson-Boltzmann implicit solvent (PB) is widely used to estimate the solvation free energies of biomolecules in molecular simulations. An optimized set of atomic radii (PB radii) is an important parameter for PB calculations, which determines the distribution of dielectric constants around the solute. We here present new PB radii for the AMBER protein force field to accurately reproduce the solvation free energies obtained from explicit solvent simulations. The presented PB radii were optimized using results from explicit solvent simulations of the large systems. In addition, we discriminated PB radii for N- and C-terminal residues from those for nonterminal residues. The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment. The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules. (c) 2014 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据