分子动力学模拟：进展与应用
Molecular dynamics simulations: advances and applications.
作者信息
Hospital Adam, Goñi Josep Ramon, Orozco Modesto, Gelpí Josep L
机构信息
Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, University of Barcelona, Barcelona, Spain.
Joint BSC-IRB Research Program in Computational Biology, University of Barcelona, Barcelona, Spain ; Barcelona Supercomputing Center, University of Barcelona, Barcelona, Spain.
出版信息
Adv Appl Bioinform Chem. 2015 Nov 19;8:37-47. doi: 10.2147/AABC.S70333. eCollection 2015.
Abstract
Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed.
摘要
分子动力学模拟已经发展成为一种成熟的技术，可有效地用于理解大分子结构与功能的关系。目前的模拟时间已接近生物学相关时间。收集到的关于大分子动态特性的信息非常丰富，足以使结构生物信息学的常规范式从研究单一结构转变为分析构象集合。在此，我们描述分子动力学的基础以及在获取此类集合方面所取得的进展。讨论了该技术在三个主要问题（变构调节、对接和结构优化）上的具体应用。
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本文引用的文献
1
PELE: Protein Energy Landscape Exploration. A Novel Monte Carlo Based Technique.
J Chem Theory Comput. 2005 Nov;1(6):1304-11. doi: 10.1021/ct0501811.
2
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.
J Chem Theory Comput. 2008 Mar;4(3):435-47. doi: 10.1021/ct700301q.
3
Approaching Elastic Network Models to Molecular Dynamics Flexibility.
J Chem Theory Comput. 2010 Sep 14;6(9):2910-23. doi: 10.1021/ct100208e.
4
Ensemble Docking from Homology Models.
J Chem Theory Comput. 2010 Aug 10;6(8):2547-57. doi: 10.1021/ct100246y. Epub 2010 Jul 16.
5
ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale.
J Chem Theory Comput. 2009 Jun 9;5(6):1632-9. doi: 10.1021/ct9000685. Epub 2009 May 21.
6
Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations.
J Chem Theory Comput. 2012 Nov 13;8(11):4707-18. doi: 10.1021/ct300494q. Epub 2012 Sep 6.
7
Application of Drug-Perturbed Essential Dynamics/Molecular Dynamics (ED/MD) to Virtual Screening and Rational Drug Design.
J Chem Theory Comput. 2012 Jul 10;8(7):2204-14. doi: 10.1021/ct300223c. Epub 2012 Jun 26.
8
Efficient Relaxation of Protein-Protein Interfaces by Discrete Molecular Dynamics Simulations.
J Chem Theory Comput. 2013 Feb 12;9(2):1222-9. doi: 10.1021/ct301039e. Epub 2012 Dec 28.
9
Accelerated molecular dynamics simulations of protein folding.
J Comput Chem. 2015 Jul 30;36(20):1536-49. doi: 10.1002/jcc.23964. Epub 2015 Jun 12.
10
Conformational processing of oncogenic v-Src kinase by the molecular chaperone Hsp90.
Proc Natl Acad Sci U S A. 2015 Jun 23;112(25):E3189-98. doi: 10.1073/pnas.1424342112. Epub 2015 Jun 8.
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