@article{CTT100920685,
  author = {Genki Kudo and Keisuke Yanagisawa and Ryunosuke Yoshino and Takatsugu Hirokawa},
  title = {AAp-MSMD: Amino Acid Preference Mapping on Protein–Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics},
  journal = {Journal of Chemical Information and Modeling},
  year = 2023,
}

@article{CTT100922719,
  author = {Ryunosuke Yoshino and Nobuaki Yasuo and Yohsuke Hagiwara and Takashi Ishida and Daniel Ken Inaoka and Yasushi Amano and Yukihiro Tateishi and Kazuki Ohno and Ichiji Namatame and Tatsuya Niimi and Masaya Orita and Kiyoshi Kita and Yutaka Akiyama and Masakazu Sekijima},
  title = {Discovery of a Hidden Trypanosoma cruzi Spermidine Synthase Binding Site and Inhibitors through In Silico, In Vitro, and X-ray Crystallography},
  journal = {ACS omega},
  year = 2023,
}

@article{CTT100869173,
  author = {Keisuke Yanagisawa and Ryunosuke Yoshino and Genki Kudo and Takatsugu Hirokawa},
  title = {Inverse Mixed-Solvent Molecular Dynamics for Visualization of the Residue Interaction Profile of Molecular Probes},
  journal = {International Journal of Molecular Sciences},
  year = 2022,
}

@article{CTT100813782,
  author = {Ryunosuke Yoshino and Nobuaki Yasuo and Masakazu Sekijima},
  title = {Molecular Dynamics Simulation reveals the mechanism by which the Influenza Cap-dependent Endonuclease acquires resistance against Baloxavir marboxil},
  journal = {Scientific Reports},
  year = 2019,
}

@article{CTT100810746,
  author = {Shuntaro Chiba and Masahito Ohue and Anastasiia Gryniukova and Petro Borysko and Sergey Zozulya and Nobuaki Yasuo and Ryunosuke Yoshino and Kazuyoshi Ikeda and Woong-Hee Shin and Daisuke Kihara and Mitsuo Iwadate and Hideaki Umeyama and Takaaki Ichikawa and Reiji Teramoto and Kun-Yi Hsin and Vipul Gupta and Hiroaki Kitano and Mika Sakamoto and Akiko Higuchi and Nobuaki Miura and Kei Yura and Masahiro Mochizuki and Chandrasekaran Ramakrishnan and A. Mary Thangakani and D. Velmurugan and M. Michael Gromiha and Itsuo Nakane and Nanako Uchida and Hayase Hakariya and Modong Tan and Hironori Nakamura and Shogo Suzuki and Tomoki Ito and Masahiro Kawatani and Kentaroh Kudoh and Sakurako Takashina and Kazuki Yamamoto and Yoshitaka Moriwaki and Keita Oda and Daisuke Kobayashi and Tatsuya Okuno and Shintaro Minami and George Chikenji and Philip Prathipati and Chioko Nagao and Attayeb Mohsen and Mari Ito and Kenji Mizuguchi and Teruki Honma and Takashi Ishida and Takatsugu Hirokawa and Yutaka Akiyama and Masakazu Sekijima.},
  title = {A prospective compound screening contest identified broader inhibitors for Sirtuin 1},
  journal = {Scientific Reports},
  year = 2019,
}

@article{CTT100783049,
  author = {Wakui, N. and Yoshino, R. and Yasuo, N. and Ohue, M. and Sekijima, M.},
  title = {Exploring the selectivity of inhibitor complexes with Bcl-2 and Bcl-XL: A molecular dynamics simulation approach},
  journal = {Journal of Molecular Graphics and Modelling},
  year = 2018,
}

@article{CTT100766244,
  author = {Shuntaro Chiba and Takashi Ishida and Kazuyoshi Ikeda and Masahiro Mochizuki and Reiji Teramoto and Y-h. Taguchi and Mitsuo Iwadate and Hideaki Umeyama and Chandrasekaran Ramakrishnan and A. Mary Thangakani and D. Velmurugan and M. Michael Gromiha and Tatsuya Okuno and Koya Kato and Shintaro Minami and George Chikenji and Shogo D. Suzuki and Keisuke Yanagisawa and Woong-Hee Shin and Daisuke Kihara and Kazuki Z. Yamamoto and Yoshitaka Moriwaki and Nobuaki Yasuo and Ryunosuke Yoshino and Sergey Zozulya and Petro Borysko and Roman Stavniichuk and Teruki Honma and Takatsugu Hirokawa and Yutaka Akiyama and Masakazu Sekijima},
  title = {An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes},
  journal = {Scientific Reports},
  year = 2017,
}

@article{CTT100766242,
  author = {Ryunosuke Yoshino and Nobuaki Yasuo and Yohsuke Hagiwara and Takashi Ishida and Daniel Ken Inaoka and Yasushi Amano and Yukihiro Tateishi and Kazuki Ohno and Ichiji Namatame and Tatsuya Niimi and Masaya Orita and Kiyoshi Kita and Yutaka Akiyama and Masakazu Sekijima},
  title = {In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease},
  journal = {Scientific Reports},
  year = 2017,
}

@inproceedings{CTT100920686,
  author = {Chie Motono and Jun Koseki and Keisuke Yanagisawa and Genki Kudo and Ryunosuke Yoshino and Takatsugu Hirokawa and Kenichiro Imai},
  title = {Cryptic site detection using machine learning based on mixed-solvent molecular dynamics simulations results},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100920687,
  author = {Jun Koseki and Chie Motono and Keisuke Yanagisawa and Genki Kudo and Ryunosuke Yoshino and Takatsugu Hirokawa and Kenichiro Imai},
  title = {Development of the Cryptic Site searching method with Mixed-solvent molecular dynamics and Topological data analyses methods},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100920692,
  author = {柳澤 渓甫 and 吉野 龍ノ介 and 工藤 玄己 and 広川 貴次},
  title = {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},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100920698,
  author = {本野 千恵 and 柳澤 渓甫 and 工藤 玄己 and 吉野 龍ノ介 and 広川 貴次 and 今井 賢一郎},
  title = {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},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100920688,
  author = {Keisuke Yanagisawa and Ryunosuke Yoshino and Genki Kudo and Takatsugu Hirokawa},
  title = {Quantitative Evaluation of Protein-Compound Substructure Interaction with Inverse Mixed-Solvent Molecular Dynamics Simulation},
  booktitle = {},
  year = 2024,
}

@inproceedings{CTT100920699,
  author = {Keisuke Yanagisawa and Ryunosuke Yoshino and Genki Kudo and Takatsugu Hirokawa},
  title = {Quantitative Evaluation of Protein-Chemical Substructure Interaction with Inverse Mixed-Solvent Molecular Dynamics Simulation},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100920701,
  author = {Keisuke Yanagisawa and Ryunosuke Yoshino and Genki Kudo and Takatsugu Hirokawa},
  title = {Quantitative Estimation of Protein-Chemical Substructure Interaction with Inverse Mixed-Solvent Molecular Dynamics Simulation},
  booktitle = {},
  year = 2023,
}

@inproceedings{CTT100783054,
  author = {Naoki Wakui and Ryunosuke Yoshino and Nobuaki Yasuo and Masahito Ohue and Masakazu Sekijima},
  title = {Exploring the selectivity of inhibitor complexes with Bcl-2 and Bcl-XL: a molecular dynamics simiulation approach},
  booktitle = {},
  year = 2017,
}