osaka-u.ac.jp
Papers 13
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Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch
Piotr Chyży, Marta Kulik, Ai Shinobu, Suyong Re, Yuji Sugita, Joanna Trylska
Proceedings of the National Academy of Sciences 2024/04/09 Research paper (scientific journal)
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The impact of inhibitor size and flexibility on the binding pathways to c-Src kinase
Ai Shinobu, Suyong Re, Yuji Sugita
2022/10/26 Research paper (scientific journal)
Publisher: Cold Spring Harbor Laboratory
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Practical Protocols for Efficient Sampling of Kinase-Inhibitor Binding Pathways Using Two-Dimensional Replica-Exchange Molecular Dynamics
Ai Shinobu, Suyong Re, Yuji Sugita
Frontiers in Molecular Biosciences Vol. 9 2022/04/29 Research paper (scientific journal)
Publisher: Frontiers Media SA
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Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins
Ai Shinobu, Chigusa Kobayashi, Yasuhiro Matsunaga, Yuji Sugita
Journal of Chemical Information and Modeling Vol. 61 No. 5 p. 2427-2443 2021/05/24 Research paper (scientific journal)
Publisher: American Chemical Society (ACS)
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Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy Calculations
Weitong Ren, Hisham M. Dokainish, Ai Shinobu, Hiraku Oshima, Yuji Sugita
The Journal of Physical Chemistry B Vol. 125 No. 11 p. 2898-2909 2021/03/25 Research paper (scientific journal)
Publisher: American Chemical Society (ACS)
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evERdock BAI: Machine-learning-guided selection of protein-protein complex structure
Kei Terayama, Ai Shinobu, Koji Tsuda, Kazuhiro Takemura, Akio Kitao
The Journal of Chemical Physics Vol. 151 No. 21 p. 215104-215104 2019/12/07 Research paper (scientific journal)
Publisher: {AIP} Publishing
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Essential ion binding residues for Na+ flow in stator complex of the Vibrio flagellar motor
Yasuhiro Onoue, Masayo Iwaki, Ai Shinobu, Yasutaka Nishihara, Hiroto Iwatsuki, Hiroyuki Terashima, Akio Kitao, Hideki Kandori, Michio Homma
Scientific Reports Vol. 9 No. 1 2019/08/02 Research paper (scientific journal)
Publisher: Springer Science and Business Media LLC
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Building a macro-mixing dual‑basin Gō model using the Multistate Bennett Acceptance Ratio
Ai Shinobu, Chigusa Kobayashi, Yasuhiro Matsunaga, Yuji Sugita
Biophysics and Physicobiology Vol. 16 p. 310-321 2019 Research paper (scientific journal)
Publisher: Biophysical Society of Japan
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Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations
Ai Shinobu, Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao
The Journal of Chemical Physics Vol. 149 No. 19 p. 195101-195101 2018/11/21 Research paper (scientific journal)
Publisher: AIP Publishing
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Proton Wire Dynamics in the Green Fluorescent Protein
Ai Shinobu, Noam Agmon
Journal of Chemical Theory and Computation Vol. 13 No. 1 p. 353-369 2017/01/10 Research paper (scientific journal)
Publisher: American Chemical Society (ACS)
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The Hole in the Barrel: Water Exchange at the GFP Chromophore
Ai Shinobu, Noam Agmon
The Journal of Physical Chemistry B Vol. 119 No. 8 p. 3464-3478 2015/02/26 Research paper (scientific journal)
Publisher: American Chemical Society (ACS)
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Visualizing Proton Antenna in a High-Resolution Green Fluorescent Protein Structure
Ai Shinobu, Gottfried J. Palm, Abraham J. Schierbeek, Noam Agmon
Journal of the American Chemical Society Vol. 132 No. 32 p. 11093-11102 2010/08/18 Research paper (scientific journal)
Publisher: American Chemical Society (ACS)
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Mapping Proton Wires in Proteins: Carbonic Anhydrase and GFP Chromophore Biosynthesis
Ai Shinobu, Noam Agmon
The Journal of Physical Chemistry A Vol. 113 No. 26 p. 7253-7266 2009/07/02 Research paper (scientific journal)
Publisher: American Chemical Society (ACS)