論文

• Genki Kudo, Keisuke Yanagisawa, Ryunosuke Yoshino, Takatsugu Hirokawa. AAp-MSMD: Amino Acid Preference Mapping on Protein–Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics, Journal of Chemical Information and Modeling, American Chemical Society, 63, 24, 7768-7777, Dec. 2023.  公式リンク  
  
• Ryunosuke Yoshino, Nobuaki Yasuo, Yohsuke Hagiwara, Takashi Ishida, Daniel Ken Inaoka, Yasushi Amano, Yukihiro Tateishi, Kazuki Ohno, Ichiji Namatame, Tatsuya Niimi, Masaya Orita, Kiyoshi Kita, Yutaka Akiyama, Masakazu Sekijima. Discovery of a Hidden Trypanosoma cruzi Spermidine Synthase Binding Site and Inhibitors through In Silico, In Vitro, and X-ray Crystallography, ACS omega, Vol. 8, No. 29, pp. 25850-25860, July 2023.
• Keisuke Yanagisawa, Ryunosuke Yoshino, Genki Kudo, Takatsugu Hirokawa. Inverse Mixed-Solvent Molecular Dynamics for Visualization of the Residue Interaction Profile of Molecular Probes, International Journal of Molecular Sciences, MDPI, Volume 23, Issue 9, 4749, Apr. 2022.  公式リンク  
  
• Ryunosuke Yoshino, Nobuaki Yasuo, Masakazu Sekijima. Molecular Dynamics Simulation reveals the mechanism by which the Influenza Cap-dependent Endonuclease acquires resistance against Baloxavir marboxil, Scientific Reports, Dec. 2019.  公式リンク  
  
• Shuntaro Chiba, Masahito Ohue, Anastasiia Gryniukova, Petro Borysko, Sergey Zozulya, Nobuaki Yasuo, Ryunosuke Yoshino, Kazuyoshi Ikeda, Woong-Hee Shin, Daisuke Kihara, Mitsuo Iwadate, Hideaki Umeyama, Takaaki Ichikawa, Reiji Teramoto, Kun-Yi Hsin, Vipul Gupta, Hiroaki Kitano, Mika Sakamoto, Akiko Higuchi, Nobuaki Miura, Kei Yura, Masahiro Mochizuki, Chandrasekaran Ramakrishnan, A. Mary Thangakani, D. Velmurugan, M. Michael Gromiha, Itsuo Nakane, Nanako Uchida, Hayase Hakariya, Modong Tan, Hironori Nakamura, Shogo Suzuki, Tomoki Ito, Masahiro Kawatani, Kentaroh Kudoh, Sakurako Takashina, Kazuki Yamamoto, Yoshitaka Moriwaki, Keita Oda, Daisuke Kobayashi, Tatsuya Okuno, Shintaro Minami, George Chikenji, Philip Prathipati, Chioko Nagao, Attayeb Mohsen, Mari Ito, Kenji Mizuguchi, Teruki Honma, Takashi Ishida, Takatsugu Hirokawa, Yutaka Akiyama, Masakazu Sekijima.. A prospective compound screening contest identified broader inhibitors for Sirtuin 1, Scientific Reports, 9, Dec. 2019.  公式リンク  
  
• Wakui, N., Yoshino, R., Yasuo, N., Ohue, M., Sekijima, M.. Exploring the selectivity of inhibitor complexes with Bcl-2 and Bcl-XL: A molecular dynamics simulation approach, Journal of Molecular Graphics and Modelling, Vol. 79, pp. 166-174, Jan. 2018.  公式リンク  
  
• Shuntaro Chiba, Takashi Ishida, Kazuyoshi Ikeda, Masahiro Mochizuki, Reiji Teramoto, Y-h. Taguchi, Mitsuo Iwadate, Hideaki Umeyama, Chandrasekaran Ramakrishnan, A. Mary Thangakani, D. Velmurugan, M. Michael Gromiha, Tatsuya Okuno, Koya Kato, Shintaro Minami, George Chikenji, Shogo D. Suzuki, Keisuke Yanagisawa, Woong-Hee Shin, Daisuke Kihara, Kazuki Z. Yamamoto, Yoshitaka Moriwaki, Nobuaki Yasuo, Ryunosuke Yoshino, Sergey Zozulya, Petro Borysko, Roman Stavniichuk, Teruki Honma, Takatsugu Hirokawa, Yutaka Akiyama, Masakazu Sekijima. An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes, Scientific Reports, Nature Publishing Group, Vol. 7, No. 12038, pp. 1-13, Sept. 2017.
• Ryunosuke Yoshino, Nobuaki Yasuo, Yohsuke Hagiwara, Takashi Ishida, Daniel Ken Inaoka, Yasushi Amano, Yukihiro Tateishi, Kazuki Ohno, Ichiji Namatame, Tatsuya Niimi, Masaya Orita, Kiyoshi Kita, Yutaka Akiyama, Masakazu Sekijima. In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease, Scientific Reports, Springer Nature, 7, July 2017.

国際会議発表 (査読なし・不明)

• Chie Motono, Jun Koseki, Keisuke Yanagisawa, Genki Kudo, Ryunosuke Yoshino, Takatsugu Hirokawa, Kenichiro Imai. Cryptic site detection using machine learning based on mixed-solvent molecular dynamics simulations results, Asia & Pacific Bioinformatics Joint Conference 2024, Oct. 2024.
• Jun Koseki, Chie Motono, Keisuke Yanagisawa, Genki Kudo, Ryunosuke Yoshino, Takatsugu Hirokawa, Kenichiro Imai. Development of the Cryptic Site searching method with Mixed-solvent molecular dynamics and Topological data analyses methods, Asia & Pacific Bioinformatics Joint Conference 2024, Oct. 2024.
• Keisuke Yanagisawa, Ryunosuke Yoshino, Genki Kudo, Takatsugu Hirokawa. Quantitative Evaluation of Protein-Compound Substructure Interaction with Inverse Mixed-Solvent Molecular Dynamics Simulation, 21st IUPAB and 62nd BSJ joint congress 2024, June 2024.  公式リンク  
  
• Naoki Wakui, Ryunosuke Yoshino, Nobuaki Yasuo, Masahito Ohue, Masakazu Sekijima. Exploring the selectivity of inhibitor complexes with Bcl-2 and Bcl-XL: a molecular dynamics simiulation approach, 4th IIT Madras-Tokyo Tech Joint Symposium on Frontiers in Bioinformatics: Large Scale Data Analysis, Resources and Drug Design, Nov. 2017.  公式リンク  
  

国内会議発表 (査読なし・不明)

• 柳澤 渓甫, 吉野 龍ノ介, 工藤 玄己, 広川 貴次. Inverse MSMDシミュレーションによるタンパク質－化合物部分構造相互作用定量的評価手法の開発, 第24回日本蛋白質科学会年会, June 2024.
• 本野 千恵, 柳澤 渓甫, 工藤 玄己, 吉野 龍ノ介, 広川 貴次, 今井 賢一郎. 共溶媒分子動力学シミュレーションによるクリプティックサイト予測, 第24回日本蛋白質科学会年会, June 2024.
• Keisuke Yanagisawa, Ryunosuke Yoshino, Genki Kudo, Takatsugu Hirokawa. Quantitative Evaluation of Protein-Chemical Substructure Interaction with Inverse Mixed-Solvent Molecular Dynamics Simulation, The 61st Annual Meeting of The Biophysical Society of Japan, Nov. 2023.  公式リンク  
  
• Keisuke Yanagisawa, Ryunosuke Yoshino, Genki Kudo, Takatsugu Hirokawa. Quantitative Estimation of Protein-Chemical Substructure Interaction with Inverse Mixed-Solvent Molecular Dynamics Simulation, Chem-Bio Informatics Society (CBI) Annual Meeting 2023, Oct. 2023.  公式リンク  
  

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