"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",,,,,,2024,Oct. "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",,,,,,2024,Oct. "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",,,,,,2024,June "–öàV Œk•á,‹g–ì —´ƒm‰î,H“¡ ŒºŒÈ,Lì ‹MŽŸ","Inverse MSMDƒVƒ~ƒ…ƒŒ[ƒVƒ‡ƒ“‚É‚æ‚éƒ^ƒ“ƒpƒNŽ¿?‰»‡•¨•”•ª\‘¢‘ŠŒÝì—p’è—Ê“I•]‰¿Žè–@‚ÌŠJ”­","‘æ24‰ñ“ú–{’`”’Ž¿‰ÈŠw‰ï”N‰ï",,,,,,2024,June "–{–ì çŒb,–öàV Œk•á,H“¡ ŒºŒÈ,‹g–ì —´ƒm‰î,Lì ‹MŽŸ,¡ˆä Œ«ˆê˜Y","‹¤—n”}•ªŽq“®—ÍŠwƒVƒ~ƒ…ƒŒ[ƒVƒ‡ƒ“‚É‚æ‚éƒNƒŠƒvƒeƒBƒbƒNƒTƒCƒg—\‘ª","‘æ24‰ñ“ú–{’`”’Ž¿‰ÈŠw‰ï”N‰ï",,,,,,2024,June "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",2023,Dec. "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",,,,,,2023,Nov. "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",,,,,,2023,Oct. "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",2022,Apr. "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",,,2019,Dec. "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",2017,Sept. "Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue,Takatsugu Hirokawa,Yutaka Akiyama","Analysis of protein docking decoys in terms of physicochemical properties of protein surfaces using rigid-body docking process","3nd IIT Madras ? Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics",,,,,,2015,Nov. "Shuntaro Chiba,Kazuyoshi Ikeda,Takashi Ishida,M. Michael Gromiha,Y-h. Taguchi,Mitsuo Iwadate,Hideaki Umeyama,Kun-Yi Hsin,Hiroaki Kitano,Kazuki Yamamoto,Nobuyoshi Sugaya,Koya Kato,Tatsuya Okuno,George Chikenji,Masahiro Mochizuki,Nobuaki Yasuo,Ryunosuke Yoshino,Keisuke Yanagisawa,Tomohiro Ban,Reiji Teramoto,Chandrasekaran Ramakrishnan,A. Mary Thangakani,D. Velmurugan,Philip Prathipati,Junichi Ito,Yuko Tsuchiya,Kenji Mizuguchi,Teruki Honma,Takatsugu Hirokawa,Yutaka Akiyama,Masakazu Sekijima","Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target",,"Scientific Reports",,"Vol. 5","No. 17209",,2015,Nov. "Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue,Takatsugu Hirokawa,Yutaka Akiyama","Analysis of amino acid properties in interaction surfaces of decoys generated by re-docking","Biophysical Society 59th Annual Meeting",,,,,,2015,Feb. "“àŒÃŠÕL”V,¼è—R—,‘åã‰ëŽj,Lì‹MŽŸ,HŽR‘×","Analysis of properties of protein-protein interaction surface areas involved in more near-native conmplexes by Re-docking scheme","‘æ52‰ñ“ú–{¶•¨•¨—Šw‰ï”N‰ï",,,,,,2014,Sept. "Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue,Takatsugu Hirokawa,Yutaka Akiyama","Re-docking scheme of protein-protein interactions for generating near-native interaction patterns in difficult docking cases","2nd IIT Madras ? Tokyo Tech Joint Symposium on Techniques and Applications of Bioinformatics",,,,,,2013,Sept.