物理化学学报 >> 2017, Vol. 33 >> Issue (7): 13541354-1365.doi: 10.3866/PKU.WHXB201704144

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分子动力学模拟技术在生物分子研究中的进展

曹了然1,张春煜2,张鼎林1,楚慧郢1,张跃斌1,李国辉1,*()   

  1. 1 中国科学院大连化学物理研究所分子模拟与设计研究组,分子反应动力学国家重点实验室,辽宁大连116023
    2 辽河油田总医院,辽宁盘锦124010
  • 收稿日期:2016-12-01 发布日期:2017-05-31
  • 通讯作者: 李国辉 E-mail:ghli@dicp.ac.cn
  • 基金资助:
    国家自然科学基金(21573217);国家自然科学基金(91430110);国家自然科学基金(31370714);国家自然科学基金(21625302)

Recent Developments in Using Molecular Dynamics Simulation Techniques to Study Biomolecules

Liao-Ran CAO1,Chun-Yu ZHANG2,Ding-Lin ZHANG1,Hui-Ying CHU1,Yue-Bin ZHANG1,Guo-Hui LI1,*()   

  1. 1 Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning Province, P. R. China
    2 Liaohe Oil Field General Hospital, Panjin 124010, Liaoning Province, P. R. China
  • Received:2016-12-01 Published:2017-05-31
  • Contact: Guo-Hui LI E-mail:ghli@dicp.ac.cn
  • About author:CAO Liao-Ran, has been working in Dr. Li's research group since 2015 and his research mainly focuses on using enhanced sampling techniques to study complex biochemical processes, including enzyme reactions and conformational change of macromolecules|ZHANG Chun-Yu, was a visiting scholar in DICP. Her research focuses on biomedicine|ZHANG Ding-Lin, received his Master degree from Jilin University in 2007. He is currently an assistant researcher in Prof. LI Guo-Hui's group since 2009. His research focuses on computational biology|CHU Hui-Ying, received her PhD degree from Jinlin University in 2009. Since 2009, she has been working in Dalian Institute of Chemical Physics, Chinese Academy of Sciences as an associate professor, a lecturer and a postdoctoral researcher. Her research interests now mainly focus on the construction of polarizable force field|ZHANG Yue-Bin, received his Ph.D degree from the key laboratory for molecular enzymology & engineering, Jilin University in 2010. From 2010-2013, he worked as a post-doc at the state key laboratory of superamolecular structure and Materials, Jilin University. From July 2013, He joined the state key laboratory of molecular reaction dynamics, the Dalianinstitute of chemical physics, Chinese Academy of Sciences. His research aims at the understanding of the physics and function of proteins, protein complexes, and other biomolecular structures at the atomic level using computer simulations|LI Guo-Hui, received his Ph.D degree from Dalian Institute of Chemical Physics in 2000, and is now working as a professor there. His research focuses on systematic methodology developments and applications on the mechanical analysis and theoretical predictions of biomolecular structures and functions, including coarse-grained model with all atomistic accuracy, polarizable molecular models and simulation strategy with a combination of software and hardware acceleration methods
  • Supported by:
    The project was supported by the National Natural Science Foundation of China(21573217);The project was supported by the National Natural Science Foundation of China(91430110);The project was supported by the National Natural Science Foundation of China(31370714);The project was supported by the National Natural Science Foundation of China(21625302)

摘要:

在当今科学探索中,分子动力学模拟作为实验的辅助,替代甚至引导,有越来越大的重要性。在这篇综述里,我们概括介绍了分子模拟领域的发展历史,特别是专注于近期的进展,包括新的分子力场,增强采样技术以及在研究生物分子体系方面的最新成果。

关键词: 分子动力学模拟, 分子力场, 增强采样, 酶促反应

Abstract:

Molecular dynamics simulation (MDS) has gained increasing importance in current-day scientific research, as the supplement, guidance, or even replacement of experiments. In this review, we briefly introduce the history of the development of molecular dynamics simulation, focusing on recent progress including new-generation force fields, modern enhanced sampling schemes, and application for the investigation of complex biomolecules.

Key words: Molecular dynamics simulation, Force field, Enhanced sampling, Enzyme reaction

MSC2000: 

  • O641