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生物分子模拟中隐式溶剂模型开发与应用的最新进展。

Recent advances in the development and application of implicit solvent models in biomolecule simulations.

作者信息

Feig Michael, Brooks Charles L

机构信息

Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA.

出版信息

Curr Opin Struct Biol. 2004 Apr;14(2):217-24. doi: 10.1016/j.sbi.2004.03.009.

Abstract

Advances have recently been made in the development of implicit solvent methodologies and their application to the modeling of biomolecules, particularly with regard to generalized Born approaches, dielectric screening function formulations and models based on solvent-accessible surface areas. Interesting new developments include more refined non-polar solvation energy estimators, and implicit methods for modeling low-dielectric and heterogeneous environments such as membrane systems. These have been successfully applied to molecular dynamics simulations, the scoring of protein conformations, and the calculation of binding affinities and folding free energy landscapes.

摘要

近年来,隐式溶剂方法的开发及其在生物分子建模中的应用取得了进展,特别是在广义玻恩方法、介电屏蔽函数公式以及基于溶剂可及表面积的模型方面。有趣的新进展包括更精细的非极性溶剂化能估计器,以及用于模拟低介电和异质环境(如膜系统)的隐式方法。这些方法已成功应用于分子动力学模拟、蛋白质构象评分、结合亲和力计算和折叠自由能景观计算。

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