Members

Research Scientist Ai Shinobu

EDUCATION

2015 Ph.D. (chemistry) The Hebrew University of Jerusalem, Israel
2009 M.Sc. (chemistry) The Hebrew University of Jerusalem, Israel
2006 B.Sc. (chemistry) The Hebrew University of Jerusalem, Israel

RESEARCH AND TEACHING EXPERIENCES

2018-present Postdoctoral researcher, RIKEN Center for Computational Science, Japan
2017-2018 Postdoctoral researcher, School of Life Science and Technology, Tokyo Institute of Technology, Japan
2017-2018 Postdoctoral researcher, Institute of Molecular Cellullar Biosciences, The University of Tokyo, Japan.
2016 Postdoctoral researcher, The Fritz Haber Research Center, The Hebrew University of Jerusalem, Israel.

PROFESSIONAL AFFILIATIONS

The biophysical society of Japan, Protein Science Society of Japan

RESEARCH PROJECTS

Development of coarse grain models

PUBLICATIONS

  1. Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins.
    Ai Shinobu, Chigusa Kobayashi, Yasuhiro Matsunaga, Yuji Sugita
    J. Chem. Inf. Model., 61, 2427–2443 (2021).
  2. 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, and Yuji Sugita
    J. Phys. Chem. B, 125,2898-2909 (2021)
  3. evERdock BAI: machine-learning-guided selection of protein-protein complex structure.
    Kei Terayama*, Ai Shinobu*, Koji Tsuda, Kazuhiro Takemura, and Akio Kitao
    J. Chem. Phys. , 151, 215104 (2019).(*equally contributed)
  4. Building a macro-mixing dual‑basin Gō model using the Multistate Bennett Acceptance Ratio.
    Ai Shinobu, Chigusa Kobayashi, Yasuhiro Matsunaga, and Yuji Sugita
    Biophys. Physicobiol. , 16, 310-321 (2019).
  5. 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, and Mchio Homma
    Sci. Rep. , 9, 11216 (2019).(*equally contributed)
  6. Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations.
    Ai Shinobu, Kazuhiro Takemura, Nobuyuki Matubayashi, and Akio Kitao
    J. Chem. Phys. , 148, 195101 (2018).
  7. Proton Wire Dynamics in the Green Fluorescent Protein.
    Ai Shinobu and Noam Agmon
    J. Chem. Theory Comput. , 13, 353-369 (2017).
  8. The Hole in the Barrel: Water Exchange at the GFP Chromophore.
    Ai Shinobu and Noam Agmon
    J. Phys. Chem. B , 119, 3464-3478 (2015).
  9. Visualizing Proton Antenna in a High-Resolution Green Fluorescent Protein Structure.
    Ai Shinobu, Gottfried J. Palm, Abraham J. Schierbeek, and Noam Agmon
    J. Am. Chem. Soc. , 132, 11093-11102 (2010). (selected as cover art)
  10. Mapping Proton Wires in Proteins: Carbonic Anhydrase and GFP Chromophore Biosynthesis.
    Ai Shinobu and Noam Agmon
    J. Phys. Chem. A , 113, 7253-7266 (2009).