GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics
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- Higo Junichi
- Graduate School of Simulation Studies, University of Hyogo
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- Kusaka Ayumi
- Institute for Protein Research, Osaka University
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- Kasahara Kota
- College of Life Sciences, Ritsumeikan University
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- Kamiya Narutoshi
- Graduate School of Simulation Studies, University of Hyogo
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- Hayato Itaya
- Graduate School of Life Sciences, Ritsumeikan University
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- Qilin Xie
- College of Pharmaceutical Sciences, Ritsumeikan University
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- Takahashi Takuya
- College of Life Sciences, Ritsumeikan University
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- Fukuda Ikuo
- Graduate School of Simulation Studies, University of Hyogo
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- Mori Kentaro
- Graduate School of Simulation Studies, University of Hyogo National Institute of Technology, Maizuru College
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- Hata Yutaka
- Graduate School of Simulation Studies, University of Hyogo
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- Fukunishi Yoshifumi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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<p>We introduced a conformational sampling method in an earlier report: The multi-dimensional virtual-system coupled molecular dynamics (mD-VcMD) enhances conformational sampling of a biomolecular system by computer simulations. Herein, new sampling method, a subzone-based mD-VcMD, is presented as an extension of mD-VcMD. Then, the subzone-based method is extended further using a genetic algorithm (GA) named the GA-guided mD-VcMD. In these methods, iterative simulation runs are performed to increase the sampled region gradually. The new methods have the following benefits: (1) They are free from a production run: i.e., all snapshots from all iterations are useful for analyses. (2) They are free from fine tuning of a weight function (probability distribution function or potential of mean force). (3) A canonical ensemble (i.e., a thermally equilibrated ensemble) is generated from a simple procedure. A thermodynamic weight is assigned to each snapshot. (4) Selective sampling can be performed for particularly addressing a poorly sampled region without breaking the proportion of the canonical ensemble if the poorly sampled conformational region emerges in sampling. By applying the methods to a simple system that involves an energy barrier between potential-energy minima, we demonstrated that the new methods have considerably higher sampling efficiency than the original mD-VcMD does.</p>
収録刊行物
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- Biophysics and Physicobiology
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Biophysics and Physicobiology 17 (0), 161-176, 2020
一般社団法人 日本生物物理学会
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詳細情報 詳細情報について
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- CRID
- 1391694356263284608
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- NII論文ID
- 130007977387
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- ISSN
- 21894779
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- 本文言語コード
- en
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- データソース種別
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- JaLC
- Crossref
- CiNii Articles
- KAKEN
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- 使用不可