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增强采样分子动力学模拟在生物分子研究中的进展
王安辉,张志超,李国辉*
作者单位E-mail
王安辉 中国科学院大连化学物理研究所分子反应动力学国家重点实验室大连 116023大连理工大学化学学院精细化工国家重点实验室大连 116024 ghli@dicp.ac.cn 
张志超 大连理工大学化学学院精细化工国家重点实验室大连 116024 ghli@dicp.ac.cn 
李国辉* 中国科学院大连化学物理研究所分子反应动力学国家重点实验室大连 116023 ghli@dicp.ac.cn 
摘要:
分子动力学模拟能够描述蛋白质分子在行使生物学功能过程中涉及的构象变化,已发展成为生物学研究中重要的计算工具. 由于生物分子的构象分布存在崎岖的自由能面,在较为复杂的生物体系的模拟中,传统的分子动力学模拟的构象采样能力受到极大限制,模拟的时间尺度与真实的生物学过程之间仍存在差距. 增强采样是解决这一问题的有效手段. 本文综述了两类增强采样方法即约束型和无约束型增强采样算法的理论基础、最新进展及其在生物分子中的典型应用,同时也简要总结了组合型增强采样算法近些年的发展.
关键词:  增强采样,伞形采样,副本交换,多元动力学,加速分子动力学
DOI:10.1063/1674-0068/cjcp1905091
分类号:
基金项目:
Advances in Enhanced Sampling Molecular Dynamics Simulations for Biomolecules
An-hui Wang,Zhi-chao Zhang,Guo-hui Li*
Abstract:
Molecular dynamics simulation has emerged as a powerful computational tool for studying biomolecules as it can provide atomic insights into the conformational transitions involved in biological functions. However, when applied to complex biological macromolecules, the conformational sampling ability of conventional molecular dynamics is limited by the rugged free energy landscapes, leading to inherent timescale gaps between molecular dynamics simulations and real biological processes. To address this issue, several advanced enhanced sampling methods have been proposed to improve the sampling efficiency in molecular dynamics. In this review, the theoretical basis, practical applications, and recent improvements of both constraint and unconstrained enhanced sampling methods are summarized. Furthermore, the combined utilizations of different enhanced sampling methods that take advantage of both approaches are also briefly discussed.
Key words:  Enhanced sampling, Umbrella sampling, Replica exchange, Metadynamics, Accelerated molecular dynamics