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Morita, Rikuri, Shigeta, Yasuteru, Harada, Ryuhei (2021) Rearrangements of Water Molecules in Parallel Cascade Selection Molecular Dynamics Enhance Structural Explorations of Proteins. Bulletin of the Chemical Society of Japan, 94 (1) 97-105 doi:10.1246/bcsj.20200174

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Reference TypeJournal (article/letter/editorial)
TitleRearrangements of Water Molecules in Parallel Cascade Selection Molecular Dynamics Enhance Structural Explorations of Proteins
JournalBulletin of the Chemical Society of Japan
AuthorsMorita, RikuriAuthor
Shigeta, YasuteruAuthor
Harada, RyuheiAuthor
Year2021 (January 15)Volume94
Issue1
PublisherThe Chemical Society of Japan
DOIdoi:10.1246/bcsj.20200174Search in ResearchGate
Generate Citation Formats
Mindat Ref. ID13206870Long-form Identifiermindat:1:5:13206870:5
GUID0
Full ReferenceMorita, Rikuri, Shigeta, Yasuteru, Harada, Ryuhei (2021) Rearrangements of Water Molecules in Parallel Cascade Selection Molecular Dynamics Enhance Structural Explorations of Proteins. Bulletin of the Chemical Society of Japan, 94 (1) 97-105 doi:10.1246/bcsj.20200174
Plain TextMorita, Rikuri, Shigeta, Yasuteru, Harada, Ryuhei (2021) Rearrangements of Water Molecules in Parallel Cascade Selection Molecular Dynamics Enhance Structural Explorations of Proteins. Bulletin of the Chemical Society of Japan, 94 (1) 97-105 doi:10.1246/bcsj.20200174
In(2021, January) Bulletin of the Chemical Society of Japan Vol. 94 (1) The Chemical Society of Japan

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Harada, Ryuhei, Shigeta, Yasuteru (2017) Dynamic Specification of Initial Structures in Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Efficiently Promotes Biologically Relevant Rare Events. Bulletin of the Chemical Society of Japan, 90 (11). 1236-1243 doi:10.1246/bcsj.20170177
Aida, Hayato, Shigeta, Yasuteru, Harada, Ryuhei (2020) Regenerations of Initial Velocities in Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Enhance the Conformational Transitions of Proteins. Chemistry Letters, 49 (7) 798-801 doi:10.1246/cl.200196
Morita, Rikuri, Shigeta, Yasuteru, Harada, Ryuhei (2024) Structural generation by inverse transformation using principal component analysis enhances conformational sampling of protein. Bulletin of the Chemical Society of Japan, 97 (8). doi:10.1093/bulcsj/uoae087
Harada, Ryuhei, Shigeta, Yasuteru (2017) Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins. Journal of Computational Chemistry, 38 (31). 2671-2674 doi:10.1002/jcc.25060
Harada, Ryuhei, Shigeta, Yasuteru (2018) How Does Friction Coefficient Affect the Conformational Sampling Efficiency of Parallel Cascade Selection Molecular Dynamics?. Chemistry Letters, 47 (9). 1119-1122 doi:10.1246/cl.180464
Morita, Rikuri, Shigeta, Yasuteru, Harada, Ryuhei (2021) Structural Variations of Metallothionein with or without Zinc Ions Elucidated by All-Atom Molecular Dynamics Simulations. The Journal of Physical Chemistry B, 125 (46) 12712-12717 doi:10.1021/acs.jpcb.1c07928
Harada, Ryuhei, Sladek, Vladimir, Shigeta, Yasuteru (2019) Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins. Journal of Chemical Information and Modeling, 59 (12) 5198-5206 doi:10.1021/acs.jcim.9b00753
Harada, Ryuhei, Aida, Hayato, Shigeta, Yasuteru (2018) The Formation of Hydrophobic Core Regulates the Protein Folding of Villin Elucidated with Parallel Cascade Selection Molecular Dynamics. Chemistry Letters, 47 (10). 1300-1303 doi:10.1246/cl.180596
Yasuda, Takunori, Morita, Rikuri, Shigeta, Yasuteru, Harada, Ryuhei (2022) Histone H3 Inhibits Ubiquitin-Ubiquitin Intermolecular Interactions to Enhance Binding to DNA Methyl Transferase 1. Journal of Molecular Biology, 434 (2) 167371pp. doi:10.1016/j.jmb.2021.167371
Yasuda, Takunori, Shigeta, Yasuteru, Harada, Ryuhei (2020) Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics. Journal of Chemical Information and Modeling, 60 (8) 4021-4029 doi:10.1021/acs.jcim.0c00580
Yasuda, Takunori, Morita, Rikuri, Shigeta, Yasuteru, Harada, Ryuhei (2022) Structural Validation by the G-Factor Properly Regulates Boost Potentials Imposed in Conformational Sampling of Proteins. Journal of Chemical Information and Modeling, 62 (14) 3442-3452 doi:10.1021/acs.jcim.2c00573
 
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