Acta Phys. -Chim. Sin. ›› 2017, Vol. 33 ›› Issue (7): 1354-1365.doi: 10.3866/PKU.WHXB201704144

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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)

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