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RIKEN Center for Computational Science Molecular Design Computational Intelligence Unit

Unit Leader: Mitsunori Ikeguchi (Ph.D.)

Research Summary

Mitsunori Ikeguchi,

The aim of Molecular Design Computational Intelligence Unit is to develop novel hybrid computational methods of molecular simulation and artificial intelligence for rational drug design. Combining artificial intelligence with molecular simulation will extend the applicability of in-silico drug design in terms of both accuracy and efficiency. In addition to the rational design of conventional small molecules, middle-sized and macro molecules are also the targets of newly developed computational methods.

Main Research Fields

  • Biological Sciences

Related Research Fields

  • Informatics
  • Medicine, Dentistry & Pharmacy

Keywords

  • molecular simulation
  • Artificial Intelligence
  • machine lerning
  • in-slilco drug design

Selected Publications

  • 1.Takashi Yoshidome, Mitsunori Ikeguchi, Masateru Ohta.:
    "Comprehensive 3D‐RISM analysis of the hydration of small molecule binding sites in ligand‐free protein structures"
    J. Comput. Chem. 41(28): 2406-2419 (2020).
  • 2.Koichiro Kato, Tomohide Masuda, Chiduru Watanabe, Naoki Miyagawa, Hideo Mizouchi, Shumpei Nagase, Kikuko Kamisaka, Kanji Oshima, Satoshi Ono, Hiroshi Ueda, Atsushi Tokuhisa, Ryo Kanada, Masateru Ohta, Mitsunori Ikeguchi, Yasushi Okuno, Kaori Fukuzawa, and Teruki Honma.:
    "High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning"
    J Chem Inf Model. 60 (7): 3361-3368 (2020).
  • 3.Shuntaro Chiba, Aki Tanabe, Makoto Nakakido, Yasushi Okuno, Kouhei Tsumoto, Masateru Ohta.:
    "Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis"
    Sci Rep. 10(1):17590 (2020).
  • 4Masao Inoue, Tomohiko Hayashi, Simon Hikiri, Mitsunori Ikeguchi, Masahiro Kinoshita.:
    "Comparison based on statistical thermodynamics between globule-to-coil transition of poly(N-isopropylacrylamide) and cold denaturation of a protein"
    J. Mol. Liq. 317, 114129 (2020).
  • 5Takahiro Muraoka, Daiki Noguchi, Rinshi S. Kasai, Kohei Sato, Ryo Sasaki, Kazuhito V. Tabata, Toru Ekimoto, Mitsunori Ikeguchi, Kiyoto Kamagata, Norihisa Hoshino, Hiroyuki Noji, Tomoyuki Akutagawa, Kazuaki Ichimura, Kazushi Kinbara.:
    "A synthetic ion channel with anisotropic ligand response"
    Nat Commun. 11(1):2924 (2020).
  • 6.Satomi Kori, Tomohiro Jimenji, Toru Ekimoto, Miwa Sato, Fumie Kusano, Takashi Oda, Motoko Unoki, Mitsunori Ikeguchi, Kyohei Arita.:
    "Serine 298 Phosphorylation in Linker 2 of UHRF1 Regulates Ligand-Binding Property of Its Tandem Tudor Domain"
    J. Mol. Biol. 432, 4061-4075 (2020).
  • 7.Shuntaro Chiba, Yasushi Okuno, Teruki Honma, Mitsunori Ikeguchi.:
    "Force-field parametrization based on radial and energy distribution functions"
    J. Comput. Chem. 40 (29): 2577-2585 (2019).
  • 8.Masao Inoue, Tomohiko, Hayashi, Simon Hikiri, Mitsunori Ikeguchi, Masahiro Kinoshita.:
    "Mechanism of globule-to-coil transition of poly(N-isopropylacrylamide) in water: Relevance to cold denaturation of a protein"
    J. Mol. Liquids, 292, 111374 (2019).
  • 9.Tatsuya Yamada, Tomohiko Hayashi, Simon Hikiri, Naohiro Kobayashi, Hiroshi Yanagawa, Mitsunori Ikeguchi, Masato Katahira, Takashi Nagata, and Masahiro Kinoshita.:
    "How does the Recently Discovered Peptide MIP Exhibit Much Higher Binding Affinity than an Anticancer Protein p53 for an Oncoprotein MDM2?"
    J. Chem. Inf. Model. 59(8) 3533–3544 (2019).
  • 10.Toru Ekimoto, Tsutomu Yamane, Mitsunori Ikeguchi.:
    "Elimination of finite-size effects on binding free energies via the warp-drive method"
    J. Chem. Theory Comput. 14, 6544-6559 (2018).

Lab Members

Principal investigator

Mitsunori Ikeguchi
Unit Leader

Core members

Tsutomu Yamane
Senior Scientist
Shuntaro Chiba
Research Scientist

Contact Information

Email: mitsunori.ikeguchi [at] riken.jp

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