2021
DOI: 10.1103/physreve.103.032404
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Enhanced sampling method with coarse graining of conformational space

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Cited by 2 publications
(3 citation statements)
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“… 46 , 47 Although one can speed up the sampling of conformational transition events by introducing biasing potential toward the target state, it tends to distort the kinetics and leads to unphysical transition pathways. 48 As a solution, Harada and Kitao developed a parallel cascade selection molecular dynamics (PaCS-MD) method based on a genetic-type algorithm, which can generate conformational transition pathways without applying biasing potential. 28 With PaCS-MD, one can sample transition pathways for protein systems involving a high free energy barrier but without sampling unphysically high-energy regions in the conformational space.…”
Section: Methodsmentioning
confidence: 99%
See 1 more Smart Citation
“… 46 , 47 Although one can speed up the sampling of conformational transition events by introducing biasing potential toward the target state, it tends to distort the kinetics and leads to unphysical transition pathways. 48 As a solution, Harada and Kitao developed a parallel cascade selection molecular dynamics (PaCS-MD) method based on a genetic-type algorithm, which can generate conformational transition pathways without applying biasing potential. 28 With PaCS-MD, one can sample transition pathways for protein systems involving a high free energy barrier but without sampling unphysically high-energy regions in the conformational space.…”
Section: Methodsmentioning
confidence: 99%
“…The down-to-up conformational transitions of the S-proteins involve a high free energy barrier, and therefore, the related timescale for sampling such rare events is far beyond the capability of conventional MD simulations. , Although one can speed up the sampling of conformational transition events by introducing biasing potential toward the target state, it tends to distort the kinetics and leads to unphysical transition pathways . As a solution, Harada and Kitao developed a parallel cascade selection molecular dynamics (PaCS-MD) method based on a genetic-type algorithm, which can generate conformational transition pathways without applying biasing potential .…”
Section: Methodsmentioning
confidence: 99%
“…尝试将类似的方法用于针对粗 粒化蛋白质结构的静电势分布与pK a 值的预测也 取得了很好的效果. 子体系的蒙特卡罗模拟和分子动力学模拟 [78][79][80][81][82][83][84][85][86][87][88] .…”
Section: 粗粒化力场构建unclassified