Conformational transition pathway and free energy analyses of proteins by parallel cascade selection molecular dynamics (PaCS-MD)
Conformational transition pathway and free energy analyses of proteins by parallel cascade selection molecular dynamics (PaCS-MD)
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DOI：
10.1063/1.4897682
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发表时间：
2014-10
期刊：
影响因子：
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通讯作者：
R. Harada;Y. Nishihara;Nobuhiko Wakai;A. Kitao
中科院分区：
文献类型：
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作者：
R. Harada;Y. Nishihara;Nobuhiko Wakai;A. Kitao
并行级联选择分子动力学(PACS-MD)是最近提出的在引入一定的目标量的条件下产生蛋白质构象转变途径的方法(R.Harada和A.Kitao，J.Chem)。物理，139,035103,2013年)。在PACS-MD中，重复短的多个独立的分子动力学模拟周期和选择下一个周期接近目标量的结构，直到模拟的结构足够接近目标为止。在小蛋白质折叠/去折叠和蛋白质大构象转变的情况下，证明了构象采样的效率。结合加权直方图分析方法或马尔可夫状态模型，进一步利用PACS-MD的结果计算自由能景观。
Parallel Cascade Selection Molecular Dynamics (PaCS-MD) was recently proposed to generate conformational transition pathways of proteins under the condition that a certain target quantity to be reached is introduced (R. Harada and A. Kitao, J. Chem. Phys., 139, 035103 2013). In PaCS-MD, the cycle of short multiple independent molecular dynamics simulations and selection of the structures close to the target quantity for the next cycle are repeated until the simulated structures move sufficiently close to the target. Conformational sampling efficiency is demonstrated in the cases of mini-protein folding/unfolding and protein large conformational transitions. The result of PaCS-MD was further utilized to calculate free energy landscape by the combination with weighted-histogram analysis method or Markov state model.