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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
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- Tran Duy Phuoc
- School of Life Science and Technology, Tokyo Institute of Technology
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- Hata Hiroaki
- School of Life Science and Technology, Tokyo Institute of Technology
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- Ogawa Takumi
- School of Life Science and Technology, Tokyo Institute of Technology
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- Taira Yuta
- School of Life Science and Technology, Tokyo Institute of Technology
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- Kitao Akio
- School of Life Science and Technology, Tokyo Institute of Technology
Bibliographic Information
- Other Title
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- 最近の研究から PaCS-MD/MSM : Parallel Cascade Selection Molecular Dynamic Simulation in Combination with Markov State Model as an Efficient non-Bias Sampling Method
- サイキン ノ ケンキュウ カラ PaCS-MD/MSM : Parallel Cascade Selection Molecular Dynamic Simulation in Combination with Markov State Model as an Efficient non-Bias Sampling Method
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Description
<p>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.</p>
Journal
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- Ensemble
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Ensemble 22 (2), 151-156, 2020-04-30
The Molecular Simulation Society of Japan