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Research
HPC- and AI-driven Drug Development Platform Division
Biomedical Computational Intelligence Unit
Biomedical Computational Intelligence Unit
Japanese
Unit Leader Yasushi Okuno
yasushi.okuno[at]riken.jp (Lab location: Kobe)- Please change [at] to @
- 2021
- Director, HPC- and AI-driven Drug Development Platform Division, Unit Leader, Biomedical Computational Intelligence Unit, Unit Leader, AI-driven Drug Discovery Collaborative Unit, RIKEN R-CCS (-present)
Representative Director, Life Intelligence Consortium (-present) - 2016
- Professor, Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University (-present)
- 2014
- Program-Specific Professor (Endowed Chair), Graduate School of Medicine, Kyoto University
- 2008
- Professor (Endowed Chair), Graduate School of Pharmaceutical Sciences, Kyoto University
- 2006
- Associate Professor, Graduate School of Pharmaceutical Sciences, Kyoto University
- 2003
- Program-Specific Assistant Professor, Graduate School of Pharmaceutical Sciences, Kyoto University
- 2000
- Ph.D. in Pharmaceutical Sciences, Kyoto University
Keyword
- Medicine
- Drug Discovery
- Artificial Intelligence
- Simulation
- Translational Research
Research summary
- Elucidation of structure, dynamics, and function of biomolecules by integrating of simulation, AI and experiments
- Development of network approach for elucidation of disease mechanisms and identification of target molecules for drug discovery
- Development of AI and simulation technologies for translational research between clinical and basic research
Main research results
- Development of AI to estimate molecular dynamics from Cryo electron microscopy images
- Estimation of gene regulatory networks by infection with new coronavirus
- Development of a new patient stratification method using Bayesian networks
- Development of graph deep learning for chemical structures
- Development of a template matching method for structural analysis of XFEL
Representative papers
- Kenichiro Takaba, Chiduru Watanabe, Atsushi Tokuhisa, Yoshinobu Akinaga, Biao Ma, Ryo Kanada, Mitsugu Araki, Yasushi Okuno, Yusuke Kawashima, Hirotomo Moriwaki, Norihito Kawashita, Teruki Honma, Kaori Fukuzawa, Shigenori Tanaka
"Protein–ligand binding affinity prediction of cyclin‐dependent kinase‐2 inhibitors by dynamically averaged fragment molecular orbital‐based interaction energy"
Journal of Computational Chemistry 43(20) 1362-1371 2022 - Atsushi Tokuhisa, Yoshinobu Akinaga, Kei Terayama, Yuji Okamoto, Yasushi Okuno
"Single-Image Super-Resolution Improvement of X-ray Single-Particle Diffraction Images Using a Convolutional Neural Network"
Journal of Chemical Information and Modeling 2022 - Nakamura K, Kojima R, Uchino E, Ono K, Yanagita M, Murashita K, Itoh K, Nakaji S, Okuno Y:
“Health improvement framework for actionable treatment planning using a surrogate Bayesian model”
Nature Communications. 12:3088, 2021.
- Matsumoto S, Ishida S, Araki M, Kato T, Terayama K, Okuno Y:
"Extraction of protein dynamics information from cryo-EM maps using deep learning"
Nature Machine Intelligence. 3:153-160, 2021.
- Tanaka, Y, Higashihara, K, Nakazawa, M.A, Yamashita F, Tamada Y, Okuno Y
"Dynamic changes in gene-to-gene regulatory networks in response to SARS-CoV-2 infection"
Scientific Reports. 11:11241, 2021.
- 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, Teruki Honma
"High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning. "
Journal of chemical information and modeling 60(7) 3361-3368 2020 - Kojima R, Ishida S, Ohta, M, Iwata H, Honma T, Okuno Y:
“kGCN: a graph-based deep learning framework for chemical structure”
Journal of Cheminformatics. 12:32, 2020.
- Tanaka Y, Tamada Y, Ikeguchi M, Yamashita F, Okuno Y:
"System-based differential gene network analysis for characterizing sample-specific subnetwork"
Biomolecules. 10(2):306, 2020.
- Tokuhisa, A, Kanada, R, Chiba, S, Terayama K, Isaka Y, Ma B, Kamiya N, Okuno Y
"Coarse-grained diffraction template matching model to retrieve multiconformational models for biomolecule structures from noisy diffraction patterns"
Journal of Chemical Information and Modeling. 60(6): 2803-2818, 2020.
- Matsumoto S, Araki M, Isaka Y, Ono F, Hirohashi K, Ohashi S, Muto M, Okuno Y:
“E487K-induced disorder in functionally relevant dynamics of mitochondrial aldehyde dehydrogenase 2”
Biophysical Journal. 119(3):628-637, 2020.
