Chen Jianhan, Brooks Charles L, Khandogin Jana
Department of Biochemistry, Kansas State University, Manhattan, KS 66506, USA.
Curr Opin Struct Biol. 2008 Apr;18(2):140-8. doi: 10.1016/j.sbi.2008.01.003. Epub 2008 Mar 4.
Implicit solvent-based methods play an increasingly important role in molecular modeling of biomolecular structure and dynamics. Recent methodological developments have mainly focused on the extension of the generalized Born (GB) formalism for variable dielectric environments and accurate treatment of nonpolar solvation. Extensive efforts in parameterization of GB models and implicit solvent force fields have enabled ab initio simulation of protein folding to native or near-native structures. Another exciting area that has benefited from the advances in implicit solvent models is the development of constant pH molecular dynamics methods, which have recently been applied to the calculations of protein pK(a) values and the studies of pH-dependent peptide and protein folding.
基于隐式溶剂的方法在生物分子结构与动力学的分子建模中发挥着越来越重要的作用。近期的方法学进展主要集中在将广义玻恩（GB）形式主义扩展到可变介电环境以及对非极性溶剂化的精确处理上。在GB模型和隐式溶剂力场的参数化方面所做的大量努力，使得能够从头开始模拟蛋白质折叠成天然或接近天然的结构。另一个受益于隐式溶剂模型进展的令人兴奋的领域是恒定pH分子动力学方法的发展，该方法最近已应用于蛋白质pK(a)值的计算以及对pH依赖性肽和蛋白质折叠的研究。
