Publications

1. Junichi Higo, Kota Kasahara, Gert-Jan Bekker, Benson Ma, Shun Sakuraba, Shinji Iida, Narutoshi Kamiya, Ikuo Fukuda, Hidetoshi Kono, Yoshifumi Fukunishi, Haruki Nakamura, "Fly-casting with ligand–sliding and orientational selection to support the complex formation of a GPCR and a middle-sized flexible molecule" 2022, Sci. Rep. 12, 13792, DOI: 10.1038/s41598-022-17920-7

2. S. Iida and Y. Fukunishi "Asymmetric dynamics of dimeric SARS-CoV-2 and SARS-CoV main proteases in an apo form: Molecular dynamics study on fluctuations of active site, catalytic dyad, and hydration water" 2021, 1, 100016, BBA advances, DOI: 10.1016/j.bbadva.2021.100016

3. S. Iida, H. K. Nakamura, T. Mashimo, Y. Fukunishi "Structural Fluctuations of Aromatic Residues in an Apo-Form Reveal Cryptic Binding Sites: Implications for Fragment-based Drug Design" 2020, 124, 45, 9977–9986 Journal of Physical Chemistry B, DOI: 10.1021/acs.jpcb.0c04963

4. Benjamin S. Hanson, Shinji Iida, Daniel J. Read, Oliver G. Harlen, Genji Kurisu, Haruki Nakamura , Sarah A. Harris "Continuum Mechanical Parameterisation of Cytoplasmic Dynein from Atomistic Simulation" 2021 Methods, DOI: 10.1016/j.ymeth.2020.01.021

5. S. Iida, T. Kawabata, K. Kasahara, H. Nakamura, and J. Higo, "Multimodal Structural Distribution of the p53 C-terminal Domain Upon Binding to S100B via a Generalised Ensemble Method: From Disorder to Extra- Disorder" , Journal of Chemical Theory and Computation 2019, 15(4), 2597-2607, DOI: 10.1021/acs.jctc.8b01042

6. S. Iida, H. Nakamura, and J. Higo, "Enhanced Conformational Sampling to Visualize a Free-energy Landscape of Protein Complex Formation" , Biochemical Journal 2016 473, 1651–62, DOI: 10.1042/BCJ20160053

7. S. Iida, T. Mashimo, T. Kurosawa, H. Hojo, H. Muta, Y. Goto, Y. Fukunishi, H. Nakamura, J. Higo "Variation of Free-energy Landscape of the p53 C-terminal Domain Induced by Acetylation: Enhanced Conformational Sampling" 2016 Journal of Computational Chemistry, 37, 2687–2700 DOI: 10.1002/jcc.24494

Research Support

1. S.Iida, "Drug Design via Machine Learning: Use of Molecular Dynamics Data", EG-J13-022018, Nov 2018-Mar 2019, funded by The Swiss State Secretariat for Education, Research and Innovation.

2. S.Iida, "Clarification of molecular recognition mechanisms of a disordered region via molecular dynamics simulation", 17J07112, Apr 2017 -Mar 2019, funded by Japan Society for the Promotion of Science (JSPS).

3. FY2021 Adoption of research proposal for supercomputer: “TSUBAME Encouragement Program for Young/Female/Younger Users”

4. FY2020 Adoption of research proposal for supercomputer: “TSUBAME Encouragement Program for Young/Female/Younger Users”

5. Young Researchers’ Exchange Programme between Japan and Switzerland 2018

6. FY2018 Adoption of research proposal for supercomputer: “TSUBAME Encouragement Program for Young/Female/Younger Users”

7. FY2016 Adoption of research proposal for supercomputer: “TSUBAME Encouragement Program for Young/Female/Younger Users”

8. FY2015 High Performance Computing Infrastructure Research. Subject: Excellent Achievement Award (Research Organization for Information Science and Technology)