Ensemble

Online ISSN : 1884-5088
Print ISSN : 1884-6750
ISSN-L : 1884-6750

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Volume 22, Issue 2

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2020 Volume 22 Issue 2 Pages 109
Published: April 30, 2020
Released on J-STAGE: April 30, 2021

DOIhttps://doi.org/10.11436/mssj.22.109

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[title in Japanese]

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2020 Volume 22 Issue 2 Pages 110-117
Published: April 30, 2020
Released on J-STAGE: April 30, 2021

DOIhttps://doi.org/10.11436/mssj.22.110

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2020 Volume 22 Issue 2 Pages 118-126
Published: April 30, 2020
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DOIhttps://doi.org/10.11436/mssj.22.118

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2020 Volume 22 Issue 2 Pages 127-133
Published: April 30, 2020
Released on J-STAGE: April 30, 2021

DOIhttps://doi.org/10.11436/mssj.22.127

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2020 Volume 22 Issue 2 Pages 134-141
Published: April 30, 2020
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DOIhttps://doi.org/10.11436/mssj.22.134

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2020 Volume 22 Issue 2 Pages 142-150
Published: April 30, 2020
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DOIhttps://doi.org/10.11436/mssj.22.142

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PaCS-MD/MSM: Parallel Cascade Selection Molecular Dynamic Simulation in Combination with Markov State Model as an Efficient non-Bias Sampling Method

Duy Phuoc Tran, Hiroaki Hata, Takumi Ogawa, Yuta Taira, Akio Kitao

2020 Volume 22 Issue 2 Pages 151-156
Published: April 30, 2020
Released on J-STAGE: April 30, 2021

DOIhttps://doi.org/10.11436/mssj.22.151

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Parallel Cascade Selection Molecular Dynamics simulation (PaCS-MD) is among the enhanced sampling methods without applying extra bias potential/force. Here we report our recent advances in applying PaCS-MD to investigate association and dissociation of protein/peptide complexes. In combination with the Markov state model (MSM), PaCS-MD/MSM exhibits its ability to predict native complex structure and calculate the binding free energy, association and dissociation rate constants of the complexes in agreement with experimental data.

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2020 Volume 22 Issue 2 Pages 157-162
Published: April 30, 2020
Released on J-STAGE: April 30, 2021

DOIhttps://doi.org/10.11436/mssj.22.157

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2020 Volume 22 Issue 2 Pages 163-168
Published: April 30, 2020
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DOIhttps://doi.org/10.11436/mssj.22.163

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2020 Volume 22 Issue 2 Pages 169-172
Published: April 30, 2020
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DOIhttps://doi.org/10.11436/mssj.22.169

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2020 Volume 22 Issue 2 Pages 173-180
Published: April 30, 2020
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DOIhttps://doi.org/10.11436/mssj.22.173

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2020 Volume 22 Issue 2 Pages 181-187
Published: April 30, 2020
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DOIhttps://doi.org/10.11436/mssj.22.181

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2020 Volume 22 Issue 2 Pages 188-191
Published: April 30, 2020
Released on J-STAGE: April 30, 2021

DOIhttps://doi.org/10.11436/mssj.22.188

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2020 Volume 22 Issue 2 Pages 192-197
Published: April 30, 2020
Released on J-STAGE: April 30, 2021

DOIhttps://doi.org/10.11436/mssj.22.192

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