Toru Ekimoto

Profile Information

Affiliation: School of Science, Graduate School of Medical Life Science Department of Medical Life Science, Yokohama City University

Degree: 博士（理学）(九州大学)

J-GLOBAL ID: 201801007451898194
researchmap Member ID: 7000023014

External link: http://www.tsurumi.yokohama-cu.ac.jp/bioinfo/

疾患・感染病関連等タンパク質の生体分子シミュレーションにより、機能発現メカニズムの分子基盤を明らかにする研究に取り組んでいる。実験と連携した手法や、スーパーコンピュータを用いた大規模計算による解析プロトコルの開発等にも取り組んでいる。

Research Interests

Research Areas

Research History

Assistant Professor, Yokohama City University International College of Arts and Sciences, Department of Medical Life Science Graduate School of Medical Life Science Department of Medical Life Science

Awards

Dec, 2018

SAR Presentation Award (Poster Presentation), 日本薬学会構造活性相関部会

浴本亨
Jun, 2017

第17回日本蛋白質科学会若手奨励賞, 日本蛋白質科学会

浴本亨

Papers

Structural basis for ligand recognition and signaling of hydroxy-carboxylic acid receptor 2.

Jae-Hyun Park, Kouki Kawakami, Naito Ishimoto, Tatsuya Ikuta, Mio Ohki, Toru Ekimoto, Mitsunori Ikeguchi, Dong-Sun Lee, Young-Ho Lee, Jeremy R H Tame …

Nature communications, 14(1) 7150-7150, Nov 6, 2023
Mandibulofacial dysostosis with alopecia results from ETAR gain-of-function mutations via allosteric effects on ligand binding.

Yukiko Kurihara, Toru Ekimoto, Christopher T Gordon, Yasunobu Uchijima, Ryo Sugiyama, Taro Kitazawa, Akiyasu Iwase, Risa Kotani, Rieko Asai, Véronique Pingault …

The Journal of clinical investigation, 133(4), Feb 15, 2023
TLR3 forms a laterally aligned multimeric complex along double-stranded RNA for efficient signal transduction

Kentaro Sakaniwa, Akiko Fujimura, Takuma Shibata, Hideki Shigematsu, Toru Ekimoto, Masaki Yamamoto, Mitsunori Ikeguchi, Kensuke Miyake, Umeharu Ohto, Toshiyuki Shimizu

Nature Communications, 14(1), Jan 11, 2023
Binding and Unbinding Pathways of Peptide Substrates on the SARS-CoV-2 3CL Protease.

Kei Moritsugu, Toru Ekimoto, Mitsunori Ikeguchi, Akinori Kidera

Journal of chemical information and modeling, 63(1) 240-250, Jan 9, 2023
Functional dynamics of SARS-CoV-2 3C-like protease as a member of clan PA.

Akinori Kidera, Kei Moritsugu, Toru Ekimoto, Mitsunori Ikeguchi

Biophysical reviews, 14(6) 1473-1485, Dec, 2022
Hybrid in vitro/in silico analysis of low-affinity protein-protein interactions that regulate signal transduction by Sema6D.

Tsubasa Tanaka, Toru Ekimoto, Meri Nagatomo, Makiko Neyazaki, Erena Shimoji, Tsutomu Yamane, Sakura Kanagawa, Rika Oi, Emiko Mihara, Junichi Takagi …

Protein science : a publication of the Protein Society, 31(11) e4452, Nov, 2022
3D-RISM-AI: A Machine Learning Approach to Predict Protein-Ligand Binding Affinity Using 3D-RISM.

Kazu Osaki, Toru Ekimoto, Tsutomu Yamane, Mitsunori Ikeguchi

The journal of physical chemistry. B, 126(33) 6148-6158, Aug 25, 2022
Structure of SARS-CoV-2 membrane protein essential for virus assembly.

Zhikuan Zhang, Norimichi Nomura, Yukiko Muramoto, Toru Ekimoto, Tomoko Uemura, Kehong Liu, Moeko Yui, Nozomu Kono, Junken Aoki, Mitsunori Ikeguchi …

Nature communications, 13(1) 4399-4399, Aug 5, 2022 Peer-reviewed
Correction to "Supramolecular Mechanosensitive Potassium Channel Formed by Fluorinated Amphiphilic Cyclophane".

Kohei Sato, Ryo Sasaki, Ryoto Matsuda, Mayuko Nakagawa, Toru Ekimoto, Tsutomu Yamane, Mitsunori Ikeguchi, Kazuhito V Tabata, Hiroyuki Noji, Kazushi Kinbara

Journal of the American Chemical Society, 144(30) 13983-13984, Aug 3, 2022
Supramolecular Mechanosensitive Potassium Channel Formed by Fluorinated Amphiphilic Cyclophane.

Kohei Sato, Ryo Sasaki, Ryoto Matsuda, Mayuko Nakagawa, Toru Ekimoto, Tsutomu Yamane, Mitsunori Ikeguchi, Kazuhito V Tabata, Hiroyuki Noji, Kazushi Kinbara

Journal of the American Chemical Society, 144(26) 11802-11809, Jun 21, 2022
Development of the force field for cyclosporine A.

Tsutomu Yamane, Toru Ekimoto, Mitsunori Ikeguchi

Biophysics and physicobiology, 19 e190045, 2022
Structure-based screening combined with computational and biochemical analyses identified the inhibitor targeting the binding of DNA Ligase 1 to UHRF1.

Satomi Kori, Yuki Shibahashi, Toru Ekimoto, Atsuya Nishiyama, Sae Yoshimi, Kosuke Yamaguchi, Satoru Nagatoishi, Masateru Ohta, Kouhei Tsumoto, Makoto Nakanishi …

Bioorganic & medicinal chemistry, 52 116500-116500, Dec 15, 2021
Allosteric Regulation of 3CL Protease of SARS-CoV-2 and SARS-CoV Observed in the Crystal Structure Ensemble.

Akinori Kidera, Kei Moritsugu, Toru Ekimoto, Mitsunori Ikeguchi

Journal of molecular biology, 433(24) 167324-167324, Dec 3, 2021
Mechanism of Vitamin D Receptor Ligand-Binding Domain Regulation Studied by gREST Simulations.

Toru Ekimoto, Takafumi Kudo, Tsutomu Yamane, Mitsunori Ikeguchi

Journal of chemical information and modeling, 61(7) 3625-3637, Jul 26, 2021
Effect of Water Molecules on the Activating S810L Mutation of the Mineralocorticoid Receptor.

Kei Takedomi, Masateru Ohta, Toru Ekimoto, Mitsunori Ikeguchi

Journal of chemical information and modeling, 61(7) 3583-3592, Jul 26, 2021
Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion.

Risako Tamura-Sakaguchi, Rie Aruga, Mika Hirose, Toru Ekimoto, Takuya Miyake, Yohei Hizukuri, Rika Oi, Mika K Kaneko, Yukinari Kato, Yoshinori Akiyama …

Acta crystallographica. Section D, Structural biology, 77(Pt 5) 645-662, May 1, 2021
Structural and dynamical insights into the PH domain of p62 in human TFIIH.

Masahiko Okuda, Toru Ekimoto, Jun-Ichi Kurita, Mitsunori Ikeguchi, Yoshifumi Nishimura

Nucleic acids research, 49(5) 2916-2930, Mar 18, 2021
Front Cover: Imidazolinium‐based Multiblock Amphiphile as Transmembrane Anion Transporter (2/2021)

Miki Mori, Kohei Sato, Toru Ekimoto, Shinichi Okumura, Mitsunori Ikeguchi, Kazuhito V. Tabata, Hiroyuki Noji, Kazushi Kinbara

Chemistry – An Asian Journal, 16(2) 110-110, Jan 18, 2021
Imidazolinium-based Multiblock Amphiphile as Transmembrane Anion Transporter.

Miki Mori, Kohei Sato, Toru Ekimoto, Shinichi Okumura, Mitsunori Ikeguchi, Kazuhito V Tabata, Hiroyuki Noji, Kazushi Kinbara

Chemistry, an Asian journal, 16(2) 147-157, Jan 18, 2021
Serine 298 Phosphorylation in Linker 2 of UHRF1 Regulates Ligand-Binding Property of Its Tandem Tudor Domain.

Satomi Kori, Tomohiro Jimenji, Toru Ekimoto, Miwa Sato, Fumie Kusano, Takashi Oda, Motoko Unoki, Mitsunori Ikeguchi, Kyohei Arita

Journal of molecular biology, 432(14) 4061-4075, Jun 26, 2020 Peer-reviewed

Misc.

X線小角散乱と分子動力学シミュレーションを組み合わせた生体分子の溶液構造解析

浴本亨, 小甲裕一, 苙口友隆, 池口満徳, 池口満徳

アンサンブル, 22(3), 2020
In vitroとin silicoの融合によるセマフォリン-プレキシンペアの結合特異性決定因子の探索

田中翼, 下地恵令奈, 永友芽里, 山根努, 浴本亨, 根谷崎牧子, 大井里香, 池口満徳, 禾晃和

日本細胞生物学会大会(Web), 71st, 2019
シグナル分子セマフォリンと受容体プレキシンの結合特異性に関する構造生物学的解析

田中翼, 永友芽里, 根谷崎牧子, 大井里香, 下地恵令奈, 山根努, 浴本亨, 池口満徳, 禾晃和

日本分子生物学会年会プログラム・要旨集(Web), 41st, 2018
MD-SAXS法によるビタミンD受容体リガンド結合ドメインの不活性型および活性阻害型の溶液構造解析

清水伸隆, 浴本亨, 穴見康昭, 伊藤俊将, 池口満徳, 山本恵子

放射光, 30(6) 264-276, Nov, 2017 Peer-reviewed
Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by a Combination Andlysis of MD Simulations and SAXS Experiments

Yasuaki Anami, Nobutaka Shimizu, Toru Ekimoto, Daichi Egawa, Toshimasa Itoh, Mitsunori Ikeguchi, Keiko Yamamoto

BIOPHYSICAL JOURNAL, 112(3) 48A-48A, Feb, 2017
神経軸索ガイダンス分子セマフォリンと受容体の相互作用のin silico解析

下地恵令奈, 山根努, 浴本亨, 禾晃和, 池口満徳

日本蛋白質科学会年会プログラム・要旨集, 17th, 2017
An Accurate and Efficient, Computational Method for the Hydration Free Energy of Large and Complex Molecules

Takashi Yoshidome, Toru Ekimoto, Nobuyuki Matubayasi, Yuichi Harano, Masahiro Kinoshita, Mitsunori Ikeguchi

BIOPHYSICAL JOURNAL, 110(3) 328A-329A, Feb, 2016 Peer-reviewed
神経軸索伸長ガイダンス分子セマフォリンと受容体プレキシンのタンパク質複合体の分子モデリング

下地恵令奈, 山根努, 浴本亨, 禾晃和, 池口満徳

日本蛋白質科学会年会プログラム・要旨集, 16th, 2016
A novel computation method of hydration free energy: A hybrid of the method of energy representation and the morphometric approach

T. Yoshidome, T. Ekimoto, N. Matubayasi, R. Roth, Y. Harano, M. Kinoshita, M. Ikeguchi

7th Mini-Symposium on Liquids, Jul, 2013
3P164 All-atom hydration analysis of the β subunit in F1-ATPase(11. Molecular motor,Poster)

Ekimoto Toru, Ikeguchi Mitsunori, Matubayasi Nobuyuki

Seibutsu Butsuri, 53(1) S239, 2013
26aTD-1 Dynamics of hard sphere systems based on the free energy landscape picture

Ekimoto Toru, Yoshimori Akira, Yoshidome Takashi, Odagaki Takashi

Meeting abstracts of the Physical Society of Japan, 65(2) 293-293, Aug 18, 2010
Separation of Dynamics in the Free Energy Landscape

T. Ekimoto, T. Odagaki, A. Yoshimori

AIP Conference Proceedings, Complex Systems, 982 211-214, 2008
20aTC-9 Relaxation processes in the Free Energy Landscape

Yoshidome T., Yoshimori A., Odagaki T.

Meeting abstracts of the Physical Society of Japan, 62(1) 349-349, Feb 28, 2007

Professional Memberships

Research Projects

Drug development for COVID-19 targeting BRD4

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Japan Society for the Promotion of Science, Apr, 2023 - Mar, 2026

Profile Information

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Research Areas

Research History

Awards

Papers

Misc.

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