Basic Information

Academic Degree

• Ph. D., Pharmacy(Osaka University)
• Master of Pharmacy(Osaka University)

Language of Instruction

• Japanese

ID,URL

• ORCID ID

  0000-0001-9329-6362

• J-Global ID

  201301036864119951

researchmap URL

• https://researchmap.jp/7000003947

Research

Research Topics, Overview of the research

• Research Topics

  Extraction of protein dynamics information from cryo-EM maps using deep learning

• Overview of the research

  Recent technical breakthroughs in cryo-EM have enabled the three dimensional structures of numerous proteins to be solved at atomic or near-atomic resolution. However, analyzing the dynamics of cryo-EM-targeted proteins is often challenging because of their large sizes and complex structural assemblies. To address the challenges, I aimed to develop an AI model to obtain dynamics information of proteins using a cryo-EM data alone.

Research Areas

• Life sciences, Structural biochemistry

Papers

• Precision spatiotemporal analysis of large-scale compound–protein interactions through molecular dynamics simulation

  Shigeyuki Matsumoto; Yuta Isaka; Ryo Kanada; Biao Ma; Mitsugu Araki; Shuntaro Chiba; Atsushi Tokuhisa; Hiroaki Iwata; Shoichi Ishida; Yoshinobu Akinaga; Kei Terayama; Ryosuke Kojima; Yohei Harada; Kazuhiro Takemura; Teruki Honma; Akio Kitao; Yasushi Okuno

  PNAS Nexus, 27 Feb. 2025, Peer-reviewed, Lead author

  
• Conversion of an agonistic anti-TNFR2 biparatopic antibody into an antagonist by insertion of peptide linkers into the hinge region

  Takuya Otsuki; Shigeyuki Matsumoto; Junso Fujita; Tomoko Miyata; Keiichi Namba; Ryo Kanada; Yasushi Okuno; Haruhiko Kamada; Hiroaki Ohno; Hiroki Akiba

  15 Feb. 2025

  
• Generating Free-energy Landscapes and Mapping Conformational Transition Pathways from cryo-EM Images using a Deep Isometric Autoencoder

  Kimihiro Yamazaki; Mutsuyo Wada; Yuichiro Wada; Atsushi Tokuhisa; Kento Ohga; Akira Nakagawa; Yoshinobu Akinaga; Yoko Sasakura; Takashi Katoh; Shigeyuki Matsumoto; Yasushi Okuno

  05 Mar. 2025

  
• kMoL: an open-source machine and federated learning library for drug discovery

  Romeo Cozac; Haris Hasic; Jun Jin Choong; Vincent Richard; Loic Beheshti; Cyrille Froehlich; Takuto Koyama; Shigeyuki Matsumoto; Ryosuke Kojima; Hiroaki Iwata; Aki Hasegawa; Takao Otsuka; Yasushi Okuno

  Journal of Cheminformatics, 25 Feb. 2025, Peer-reviewed

  
• Receptor-independent regulation of Gα13 by alpha-1-antitrypsin C-terminal peptides

  Yonghak Park; Shigeyuki Matsumoto; Kosuke Ogata; Biao Ma; Ryo Kanada; Yuta Isaka; Norihito Arichi; Xiaowen Liang; Ritsuko Maki; Tohru Kozasa; Yasushi Okuno; Hiroaki Ohno; Yasushi Ishihama; Fumiko Toyoshima

  Journal of Biological Chemistry, Dec. 2024, Peer-reviewed, Corresponding author

  
• Constructing a graph neural network-based artificial intelligence model to predict drug-induced phospholipidosis potential

  Yoshinobu Igarashi; Aki Hasegawa; Shigeyuki Matsumoto; Hiroaki Iwata; Ryosuke Kojima; Yasushi Okuno; Hiroshi Yamada

  Fundamental Toxicological Sciences, Nov. 2024, Peer-reviewed

  
• Synergistic involvement of the NZF domains of the LUBAC accessory subunits HOIL-1L and SHARPIN in the regulation of LUBAC function

  Yusuke Toda; Hiroaki Fujita; Koshiki Mino; Takuto Koyama; Seiji Matsuoka; Toshie Kaizuka; Mari Agawa; Shigeyuki Matsumoto; Akiko Idei; Momoko Nishikori; Yasushi Okuno; Hiroyuki Osada; Minoru Yoshida; Akifumi Takaori-Kondo; Kazuhiro Iwai

  Cell Death & Disease, 11 Nov. 2024, Peer-reviewed

  Access this paper :

  
• cryoMDM; Molecular simulation Driven structural Matching Approach to Estimate Variety of Atomic Three-dimensional Model Based on Noisy cryoEM Single Particle Images.

  Atsushi Tokuhisa; Yoshinobu Akinaga; Yoko Sasakura; Kei Terayama; Shigeyuki Matsumoto; Takayuki Kato; Yasushi Okuno

  01 Nov. 2024

  
• Molecular Dynamics Unveils Multiple-Site Binding of Inhibitors with Reduced Activity on the Surface of Dihydrofolate Reductase

  Mitsugu Araki; Toru Ekimoto; Kazuhiro Takemura; Shigeyuki Matsumoto; Yunoshin Tamura; Hironori Kokubo; Gert-Jan Bekker; Tsutomu Yamane; Yuta Isaka; Yukari Sagae; Narutoshi Kamiya; Mitsunori Ikeguchi; Yasushi Okuno

  Journal of the American Chemical Society, 12 Oct. 2024, Peer-reviewed

  
• Developing a GNN-based AI model to predict mitochondrial toxicity using the bagging method

  Yoshinobu Igarashi; Ryosuke Kojima; Shigeyuki Matsumoto; Hiroaki Iwata; Yasushi Okuno; Hiroshi Yamada

  The Journal of Toxicological Sciences, 2024, Peer-reviewed

  
• A macrocyclic kinase inhibitor overcomes triple resistant mutations in EGFR-positive lung cancer

  Mai Suzuki; Ken Uchibori; Tomoko Oh-hara; Yumi Nomura; Ryusei Suzuki; Ai Takemoto; Mitsugu Araki; Shigeyuki Matsumoto; Yukari Sagae; Mutsuko Kukimoto-Niino; Yusuke Kawase; Mikako Shirouzu; Yasushi Okuno; Makoto Nishio; Naoya Fujita; Ryohei Katayama

  npj Precision Oncology, 23 Feb. 2024, Peer-reviewed

  
• ChemGLaM: Chemical-Genomics Language Models for Compound-Protein Interaction Prediction

  Takuto Koyama; Hayato Tsumura; Shigeyuki Matsumoto; Ryunosuke Okita; Ryosuke Kojima; Yasushi Okuno

  15 Feb. 2024

  
• Small-molecule RAS/RAF Binding Inhibitors Allosterically Disrupt RAF Conformation and Exert Efficacy Against a Broad Spectrum of RAS-driven Cancers

  Fumi Shima; Yoko Yoshikawa; Yoshiteru Makino; Hirokazu Kubota; Takashi Kawamura; Shigeyuki Matsumoto; Hitomi Yuki; Akira Shibaike; Megumi Okamura; Tomoyo Okada; Manabu Horikawa; Kazumasa Horie; Michiyo Koyanagi-Aoi; Takashi Aoi; Tohru Kataoka; Teruki Honma; Takashi Kumasaka; Hiroo Koyama

  23 Jan. 2024

  
• VGAE-MCTS: A New Molecular Generative Model Combining the Variational Graph Auto-Encoder and Monte Carlo Tree Search

  Hiroaki Iwata; Taichi Nakai; Takuto Koyama; Shigeyuki Matsumoto; Ryosuke Kojima; Yasushi Okuno

  Journal of Chemical Information and Modeling, 22 Nov. 2023, Peer-reviewed

  
• Quantitative analysis of protein dynamics using a deep learning technique combined with experimental cryo-EM density data and MD simulations

  Shigeyuki Matsumoto; Shoichi Ishida; Kei Terayama; Yasuhshi Okuno

  Biophysics and Physicobiology, Jun. 2023, Peer-reviewed, Lead author, Corresponding author

  
• Improving Compound–Protein Interaction Prediction by Self-Training with Augmenting Negative Samples

  Takuto Koyama; Shigeyuki Matsumoto; Hiroaki Iwata; Ryosuke Kojima; Yasushi Okuno

  Journal of Chemical Information and Modeling, 17 Jul. 2023, Peer-reviewed, Corresponding author

  Access this paper :

  
• クライオEM密度マップからのタンパク質ダイナミクス情報推定

  寺山 慧; 石田 祥一; 松本 篤幸; 奥野 恭史

  生物工学会誌, Nov. 2022, Invited

  
• Novel Calcium-Binding Ablating Mutations Induce Constitutive RET Activity and Drive Tumorigenesis.

  Junya Tabata; Takashi Nakaoku; Mitsugu Araki; Ryunosuke Yoshino; Shinji Kohsaka; Ayaka Otsuka; Masachika Ikegami; Ayako Ui; Shin-Ichiro Kanno; Keiko Miyoshi; Shigeyuki Matsumoto; Yukari Sagae; Akira Yasui; Masakazu Sekijima; Hiroyuki Mano; Yasushi Okuno; Aikou Okamoto; Takashi Kohno

  Cancer research, 27 Sep. 2022, Peer-reviewed

  Access this paper :

  
• Discovery of Small-Molecule Ras Inhibitors that Display Antitumor Activity by Interfering with Ras·GTP-Effector Interaction

  Fumi Shima; Yoko Yoshikawa; Shigeyuki Matsumoto; Tohru Kataoka

  Enzymes, 2013, Peer-reviewed

  
• 2P052 Solution Structure of Variable-type Domain of Receptor for Advanced Glycation Endproducts(29. Protein structure and dynamics (II),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

  Matsumoto Shigeyuki; Yoshida Takuya; Murata Hiroko; Yamamoto Hiroshi; Kobayashi Yuji; Ohkubo Tadayasu

  Seibutsu Butsuri, 2006

  
• QAEmap: A Novel Local Quality Assessment Method for Protein Crystal Structures Using Machine Learning

  Ikuko Miyaguchi; Miwa Sato; Akiko Kashima; Hiroyuki Nakagawa; Yuichi Kokabu; Biao Ma; Shigeyuki Matsumoto; Atsushi Tokuhisa; Masateru Ohta; Mitsunori Ikeguchi

  09 Jul. 2021

  
• Extraction of Protein Dynamics Hidden in Cryo-EM Maps Using Deep Learning

  Shigeyuki MATSUMOTO; Kei TERAYAMA; Yasushi OKUNO

  Seibutsu Butsuri, Jun. 2022, Peer-reviewed, Lead author

  Access this paper :

  
• Integrated approach to functional analysis of an ERBB2 variant of unknown significance detected by a cancer gene panel test

  Yohei Harada; Akemi Sato; Mitsugu Araki; Shigeyuki Matsumoto; Yuta Isaka; Yukari Sagae; Tomonori Abe; Yasuko Aoyagi; Eisaburo Sueoka; Yasushi Okuno; Shinya Kimura; Naoko Sueoka-Aragane

  Cellular Oncology, 08 Jan. 2022, Peer-reviewed

  
• Machine learning to estimate the local quality of protein crystal structures

  Ikuko Miyaguchi; Miwa Sato; Akiko Kashima; Hiroyuki Nakagawa; Yuichi Kokabu; Biao Ma; Shigeyuki Matsumoto; Atsushi Tokuhisa; Masateru Ohta; Mitsunori Ikeguchi

  Scientific Reports, Dec. 2021, Peer-reviewed

  
• Oncogenic mutations Q61L and Q61H confer active form-like structural features to the inactive state (state 1) conformation of H-Ras protein

  Shigeyuki Matsumoto; Haruka Taniguchi-Tamura; Mitsugu Araki; Takashi Kawamura; Ryo Miyamoto; Chiemi Tsuda; Fumi Shima; Takashi Kumasaka; Yasushi Okuno; Tohru Kataoka

  Biochemical and Biophysical Research Communications, Aug. 2021, Peer-reviewed, Lead author

  
• Structure-Based de Novo Molecular Generator Combined with Artificial Intelligence and Docking Simulations

  Biao Ma; Kei Terayama; Shigeyuki Matsumoto; Yuta Isaka; Yoko Sasakura; Hiroaki Iwata; Mitsugu Araki; Yasushi Okuno

  Journal of Chemical Information and Modeling, 09 Jul. 2021, Peer-reviewed

  
• Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics

  Mitsugu Araki; Shigeyuki Matsumoto; Gert-Jan Bekker; Yuta Isaka; Yukari Sagae; Narutoshi Kamiya; Yasushi Okuno

  Nature Communications, May 2021, Peer-reviewed

  Access this paper :

  
• Microsecond-timescale MD simulation of EGFR minor mutation predicts the structural flexibility of EGFR kinase core that reflects EGFR inhibitor sensitivity

  Takahiro Yoshizawa; Ken Uchibori; Mitsugu Araki; Shigeyuki Matsumoto; Biao Ma; Ryo Kanada; Yosuke Seto; Tomoko Oh-hara; Sumie Koike; Ryo Ariyasu; Satoru Kitazono; Hironori Ninomiya; Kengo Takeuchi; Noriko Yanagitani; Satoshi Takagi; Kazuma Kishi; Naoya Fujita; Yasushi Okuno; Makoto Nishio; Ryohei Katayama

  npj Precision Oncology, Apr. 2021, Peer-reviewed

  
• Extraction of protein dynamics information from cryo-EM maps using deep learning

  Shigeyuki Matsumoto; Shoichi Ishida; Mitsugu Araki; Takayuki Kato; Kei Terayama; Yasushi Okuno

  Nature Machine Intelligence, 04 Feb. 2021, Peer-reviewed, Lead author

  
• E487K-Induced Disorder in Functionally Relevant Dynamics of Mitochondrial Aldehyde Dehydrogenase 2

  Shigeyuki Matsumoto; Mitsugu Araki; Yuta Isaka; Fumie Ono; Kenshiro Hirohashi; Shinya Ohashi; Manabu Muto; Yasushi Okuno

  Biophysical Journal, Aug. 2020, Peer-reviewed, Lead author

  
• Landscape and function of multiple mutations within individual oncogenes

  Yuki Saito; Junji Koya; Mitsugu Araki; Yasunori Kogure; Sumito Shingaki; Mariko Tabata; Marni B. McClure; Kota Yoshifuji; Shigeyuki Matsumoto; Yuta Isaka; Hiroko Tanaka; Takanori Kanai; Satoru Miyano; Yuichi Shiraishi; Yasushi Okuno; Keisuke Kataoka

  Nature, Jun. 2020, Peer-reviewed

  
• Improvement in predicting drug sensitivity changes associated with protein mutations using a molecular dynamics based alchemical mutation method

  Fumie Ono; Shuntaro Chiba; Yuta Isaka; Shigeyuki Matsumoto; Biao Ma; Ryohei Katayama; Mitsugu Araki; Yasushi Okuno

  Scientific Reports, Feb. 2020, Peer-reviewed

  
• Molecular Basis for Allosteric Inhibition of GTP-Bound H-Ras Protein by a Small-Molecule Compound Carrying a Naphthalene Ring

  Shigeyuki Matsumoto; Toshiki Hiraga; Yuki Hayashi; Yoko Yoshikawa; Chiemi Tsuda; Mitsugu Araki; Masahiro Neya; Fumi Shima; Tohru Kataoka

  Biochemistry, 11 Sep. 2018, Peer-reviewed, Lead author

  
• Structural transition of solvated H-Ras/GTP revealed by molecular dynamics simulation and local network entropy

  Shota Matsunaga; Yuta Hano; Yuta Saito; Kazuhiro J. Fujimoto; Takashi Kumasaka; Shigeyuki Matsumoto; Tohru Kataoka; Fumi Shima; Shigenori Tanaka

  JOURNAL OF MOLECULAR GRAPHICS & MODELLING, Oct. 2017, Peer-reviewed

  
• Structural basis for intramolecular interaction of post-translationally modified H-Ras.GTP prepared by protein ligation

  Haoliang Ke; Shigeyuki Matsumoto; Yosuke Murashima; Haruka Taniguchi-Tamura; Ryo Miyamoto; Yoko Yoshikawa; Chiemi Tsuda; Takashi Kumasaka; Eiichi Mizohata; Hironori Edamatsu; Tohru Kataoka

  FEBS LETTERS, Aug. 2017, Peer-reviewed

  
• Molecular Mechanism for Conformational Dynamics of Ras.GTP Elucidated from In-Situ Structural Transition in Crystal

  Shigeyuki Matsumoto; Nao Miyano; Seiki Baba; Jingling Liao; Takashi Kawamura; Chiemi Tsuda; Azusa Takeda; Masaki Yamamoto; Takashi Kumasaka; Tohru Kataoka; Fumi Shima

  SCIENTIFIC REPORTS, May 2016, Peer-reviewed, Lead author

  
• Current status of the development of Ras inhibitors

  Fumi Shima; Shigeyuki Matsumoto; Yoko Yoshikawa; Takashi Kawamura; Masayuki Isa; Tohru Kataoka

  Journal of Biochemistry, Aug. 2015, Peer-reviewed

  
• In silico discovery of small-molecule Ras inhibitors that display antitumor activity by blocking the Ras-effector interaction

  Fumi Shima; Yoko Yoshikawa; Min Ye; Mitsugu Araki; Shigeyuki Matsumoto; Jingling Liao; Lizhi Hu; Takeshi Sugimoto; Yuichi Ijiri; Azusa Takeda; Yuko Nishiyama; Chie Sato; Shin Muraoka; Atsuo Tamura; Tsutomu Osoda; Ken-ichiro Tsuda; Tomoya Miyakawa; Hiroaki Fukunishi; Jiro Shimada; Takashi Kumasaka; Masaki Yamamoto; Tohru Kataoka

  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, May 2013, Peer-reviewed

  
• Solution Structure of the Variable-Type Domain of the Receptor for Advanced Glycation End Products: New Insight into AGE−RAGE Interaction†,‡

  Shigeyuki Matsumoto; Takuya Yoshida; Hiroko Murata; Shusaku Harada; Naoko Fujita; Shota Nakamura; Yasuhiko Yamamoto; Takuo Watanabe; Hideto Yonekura; Hiroshi Yamamoto; Tadayasu Ohkubo; Yuji Kobayashi

  Biochemistry, 25 Nov. 2008, Peer-reviewed, Lead author

  
• Enhanced Conformational Sampling with an Adaptive Coarse-Grained Elastic Network Model Using Short-Time All-Atom Molecular Dynamics

  Ryo Kanada; Kei Terayama; Atsushi Tokuhisa; Shigeyuki Matsumoto; Yasushi Okuno

  Journal of Chemical Theory and Computation, 24 Mar. 2022, Peer-reviewed

  

Misc.

• AI用学習データ作成のための高・低分解能の蛋白質結晶構造比較

  宮口郁子; 鹿島亜季子; 佐藤美和; 中田一人; 馬彪; 松本篤幸; 徳久淳師; 大田雅照; 池口満徳

  日本細胞生物学会大会(Web), 2019

  
• Research on pocket prediction using 3D-CNN

  馬場剛史; 小甲裕一; 佐藤美和; 中川寛之; 宮口郁子; MA Biao; 松本篤幸; 徳久淳師; 大田雅照; 池口満徳; 池口満徳

  構造活性相関シンポジウム講演要旨集, 2019

  
• SACLA,SPring-8並びにNMRを用いた低分子量Gタンパク質RasのGTP加水分解過程における動的構造解析

  佐伯茉帆; 槇野義輝; 松本篤幸; 河村高志; 南後恵理子; 熊坂崇; 島扶美

  日本分子生物学会年会プログラム・要旨集(Web), 2020

  
• Novel Insights into the Structural Perturbation Induced by the Oncogenic Mutations, Q61L and Q61H, in Ras State 1

  Shigeyuki Matsumoto; Haruka Taniguchi-Tamura; Mitsugu Araki; Takashi Kawamura; Ryo Miyamoto; Chiemi Tsuda; Yasushi Okuno; Fumi Shima; Takashi Kumasaka; Tohru Kataoka

  BIOPHYSICAL JOURNAL, Feb. 2020

  
• 分子動力学計算を用いたアルデヒド脱水素酵素2(ALDH2)非活性型変異体の動的立体構造特性の解析

  松本篤幸; 荒木望嗣; 井阪悠太; 奥野恭史; 奥野恭史

  日本細胞生物学会大会(Web), 2019

  
• rasがん遺伝子産物の新規立体構造情報を利用した分子標的がん治療薬の開発

  Nishigori Chikako; Shima Fumi; 熊坂崇; Matsumoto Shigeyuki; Yoshikawa Yoko; 山本雅貴; Kataoka Tohru

  日本放射光学会誌 放射光, 2014, Peer-reviewed

  

Presentations

• Practical Evaluation of Protein-Compound Interactions with Computational Approaches

  Shigeyuki Matsumoto

  The 97th Annual Meeting of the Japanese Pharmacological Society, 14 Dec. 2023, Invited

  
• Iterative Data Augmentation of near boundary negative samples Compound-Protein Interaction Prediction

  Takuto Koyama; Shigeyuki Matsumoto; Hiroaki Iwata; Ryosuke Kojima; Yasushi Okuno

  Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB), 24 Jul. 2023

  
• 生命科学におけるAI・シミュレーション・実験融合. メディカルAIコース

  松本篤幸

  メディカルAI, 25 Oct. 2022, Invited

  
• Extracting protein dynamics from cryo-EM density maps by combining MD simulations and a machine learning technique.

  松本篤幸

  MOEフォーラム2022, 13 Oct. 2022, Invited

  
• Extracting protein dynamics from experimental cryo-EM maps using a machine learning technique combining with MD simulations.

  松本篤幸; 石田祥一; 寺山慧; 奥野恭史

  第60回日本生物物理学会年会, 28 Sep. 2022, Invited

  
• スーパーコンピューター「富岳」で挑む 新型コロナウイルス治療薬の探索

  松本篤幸

  【先端人シリーズvol.1】スーパーコンピュータで切り拓く健康と福祉の向上, 09 Dec. 2021, Invited

  
• Challenges in Large-scale MD-based Docking Study Targeting SARS-CoV-2 Proteins on Fugaku

  Shigeyuki Matsumoto

  Supercomputing Asia 2021, 03 Mar. 2021, Invited

  
• Challenges in Large-scale MD-based Docking Study Targeting SARS-CoV-2 Proteins on Fugaku

  Shigeyuki Matsumoto

  The 1st Fugaku Bio-supercomputing Workshop on Cellular-scale Molecular Dynamics Simulations, 07 Jan. 2021, Invited

  
• 深層学習技術による cryo-EM密度マップデータに隠された動的情報の抽出

  松本篤幸

  第一回クライオ電子顕微鏡画像からの高度情報処理研究会, 23 Oct. 2020, Invited

  
• Sotase Aを利用した翻訳後脂質修飾型Rasの産生と構造物学研究

  村嶋 陽亮; 柯 浩亮; Matsumoto Shigeyuki; Edamatsu Hironori; Kataoka Tohru

  第14回次世代を担う若手のためのフィジカル・ファーマフォーラム, Aug. 2016, 日本薬学会物理系薬学部会

  
• Crystal Mounting Method using Humid Air and Hydrophilic Glue Coating For Ambient and Cryogenic Experiments

  Takashi Kumasaka; Masaki Yamamoto; Kataoka Tohru; Shima Fumi; Matsumoto Shigeyuki; Kawamura Takashi; Nobuo Kamiya; Yasufumi Umena; Naoto Yagi; Seiki Baba

  2015 Annual Meeting of the American Crystallographic Association, Jul. 2015, American Crystallographic Association, Invited

  
• 試料雰囲気湿度調整によるRasタンパク質の結晶内構造転移

  熊坂 崇; 馬場 清喜; 宮野 菜央; Kawamura Takashi; Matsumoto Shigeyuki; 山本 雅貴; Kataoka Tohru; Shima Fumi

  第15回日本蛋白質科学会年会, Jun. 2015, 日本蛋白質科学会

  
• GTP結合型H-RasのState 1結晶構造情報に基づく立体構造遷移機構の解明

  Matsumoto Shigeyuki; 宮野 菜央; 馬場 清喜; Liao Jingling; 竹田 あずさ; 山本 雅貴; 熊坂 崇; Kataoka Tohru; Shima Fumi

  第15回日本蛋白質科学会年会, Jun. 2015, 日本蛋白質科学会

  
• GTP結合型H-Rasの活性調節に関与する立体構造遷移メカニズムの解明

  Matsumoto Shigeyuki

  YIAヤングインベスティゲーターアワード, Oct. 2014, 社団法人 神緑会(神戸大学医学部医学科同窓会)

  

Books and Other Publications

• AI・シミュレーションが切り拓くドラッグリポジショニング

  松本篤幸; 岩田浩明; 奥野恭史, Joint work

  北隆館, Dec. 2024

  
• 大規模MD計算によるCOVID-19治療薬探索

  松本篤幸, Contributor, 巻頭グラビア

  北隆館, 25 Jan. 2023

  
• クライオ電子顕微鏡計測データからタンパク質の柔らかさを推定するAIシステム「DEFMap」の開発

  松本篤幸; 徳久淳師, Contributor, 第7章第1節

  エヌ・ティー・エヌ, 20 Jan. 2023

  Find Kyoto University's collection of books :

  
• AI・シミュレーションによる薬剤開発の迅速化

  田中良尚; 松本篤幸; 奥野恭史, Joint work

  羊土社, Aug. 2022

  
• rasがん遺伝子産物Rasを分子標的としたがん治療薬開発の現状

  島扶美; 吉川陽子; 松本篤幸; 片岡徹, Joint work

  2014

  
• The Enzymes, Vol. 34, Inhibitors of the Ras superfamily G-proteins, Part B / Discovery of Small-Molecule Ras Inhibitors that Display Antitumor Activity by Interfering with Ras･GTP?Effector Interaction

  Yoshikawa Yoko; Matsumoto Shigeyuki; Kataoka Tohru, Others

  Elsevier Inc., Dec. 2013, Not refereed

  

Industrial Property Rights

• 特願2021-125013, Ras/Raf結合阻害化合物

  島扶美; 吉川陽子; 松本篤幸; 槇野義輝; 窪田浩一; 幸瞳; 熊坂崇; 河村高志

  

External funds: Kakenhi

• Elucidation of functional mechanism based on the dynamic properties for the ongene products Ras

  Grant-in-Aid for Young Scientists (B)

  Kyoto University;Institute of Physical and Chemical Research;Kobe University

  Shigeyuki Matsumoto

  From 01 Apr. 2017, To 31 Mar. 2022, Project Closed

  Ras;がん変異体;X線結晶構造解析;分子動力学計算;動的平衡;state transition;分子動力学シミュレーション;立体構造;State遷移;ダイナミクス;NMR

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-17K15106/
• Structural study on the role of post-translational lipid modifications of the small G protein Ras

  Grant-in-Aid for Scientific Research (B)

  Kobe University

  TOHRU KATAOKA

  From 01 Apr. 2014, To 31 Mar. 2017, Project Closed

  シグナル伝達;蛋白質;癌;脂質;高分子構造・物性

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-26293065/
• Research on the molecular basis of conformational dynamics of oncogene product Ras for application to the development of its specific inhibitors

  Grant-in-Aid for Scientific Research (B)

  Kobe University

  fumi shima

  From 01 Apr. 2014, To 31 Mar. 2017, Project Closed

  医薬分子設計;分子標的薬;がん;シグナル伝達;がん遺伝子;癌

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-26293026/
• 深層学習技術を用いた動的情報からの化合物ータンパク質結合親和性の抽出

  Grant-in-Aid for Scientific Research (C)

  Basic Section 43020:Structural biochemistry-related

  Kyoto University

  松本 篤幸

  From 01 Apr. 2022, To 31 Mar. 2026, Granted

  分子動力学計算;親和性予測;深層学習;結合親和性予測;低分子化合物

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-22K06112/
• cryoEM-NMR融合構造解析の確立

  Grant-in-Aid for Challenging Research (Pioneering)

  Medium-sized Section 43:Biology at molecular to cellular levels, and related fields

  Osaka University

  加藤 貴之

  From 30 Jun. 2022, To 31 Mar. 2025, Granted

  クライオ電子顕微鏡;単粒子解析;NMR;ハイブリッド構造解析;融合構造解析;電子顕微鏡

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-22K18359/
• フィロウイルスの増殖機構の分子構造基盤の解明と制御法の開発

  Grant-in-Aid for Scientific Research (A)

  Medium-sized Section 49:Pathology, infection/immunology, and related fields

  Kyoto University

  野田 岳志

  From 01 Apr. 2024, To 31 Mar. 2027, Granted

  エボラウイルス;ヌクレオカプシド;抗ウイルス薬

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-24H00609/