"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.
"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.
"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",,,,,,2024,June
"Masatake Sugita,Takuya Fujie,Yudai Noso,Keisuke Yanagisawa,Masahito Ohue,Yutaka Akiyama","Development and Application of a Protocol for Predicting Membrane Permeability of Cyclic Peptides Based on Molecular Dynamics Simulations","21st IUPAB and 62nd BSJ joint congress 2024",,"American Chemical Society",,,,2024,June
"清水 正義,柳澤 渓甫,秋山 泰","有望なフラグメント空間配置対に基づく化合物プレスクリーニング手法の開発","情報処理学会 第148回MPS・第78回BIO合同研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2024-BIO-78","  38","  1-8",2024,June
"赤木 果歩,柳澤 渓甫,秋山 泰","共溶媒分子動力学法による化合物ドッキング向けのバイアス情報の取得","情報処理学会 第148回MPS・第78回BIO合同研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2024-BIO-78","  37","  1-8",2024,June
"杉田 昌岳,藤江 拓哉,能祖 雄大,柳澤 渓甫,大上 雅史,秋山 泰","拡張アンサンブル分子動力学シミュレーションに基づいた環状ペプチドの膜透過性予測技術の開発と応用","第24回日本蛋白質科学会年会",,,,,,2024,June
"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",,,,,,2024,June
"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
"Keisuke Yanagisawa,Takuya Fujie,Kazuki Takabatake,Yutaka Akiyama","QUBO Problem Formulation of Fragment-Based Protein?Ligand Flexible Docking",,"Entropy","MDPI","  26",,,2024,Apr.
"布部 絢子,柳澤 渓甫,秋山 泰","フラグメントに基づくバーチャルスクリーニングへの利用などを目指したフラグメント集合の選定","情報処理学会 第77回BIO合同研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2024-BIO-77","  31","  1-7",2024,Mar.
"能祖雄大,杉田昌岳,藤江拓哉,柳澤渓甫,秋山泰","分子動力学シミュレーション軌跡データから抽出した位置依存特徴量を活用した環状ペプチドの膜透過性予測","第147回MPS・第77回BIO合同研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2024-BIO-77","  16","  1-8",2024,Mar.
"李 佳男,柳澤 渓甫,秋山 泰","CycPeptMP：マルチレベルの分子特徴とデータ拡張による環状ペプチドの膜透過性予測手法の開発","第147回MPS・第77回BIO合同研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2024-BIO-77","  15","  1-8",2024,Mar.
"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.
"Masatake Sugita,Takuya Fujie,Keisuke Yanagisawa,Masahito Ohue,Yutaka Akiyama","Development of a Protocol for Predicting Membrane Permeability of Cyclic Peptides Based on Molecular Dynamics Simulations","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.
"柳澤 渓甫","薬剤設計のためにはAlphaFoldはまだまだ足りない","第12回生命医薬情報学連合大会 (IIBMP2023)",,,,,,2023,Sept.
"渡辺銀河,柳澤渓甫,秋山 泰","標的RNAの高次構造予測に基づく低活性ASO候補配列の推測","情報処理学会 第143回MPS・第74回BIO合同研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-74","  36","  1-8",2023,June
"李 佳男,柳澤 渓甫,杉田 昌岳,藤江 拓哉,大上 雅史,秋山 泰","CycPeptMPDB：包括的な環状ペプチド膜透過率データベースの開発","情報処理学会 第143回MPS・第74回BIO合同研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2023-BIO-74","  38","  1-8",2023,June
"齋藤那哉,柳澤渓甫,秋山 泰","フラグメント対の相対位置から検索可能な化合物立体配座データベースの構築","情報処理学会 第143回MPS・第74回BIO合同研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-74","  37","  1-8",2023,June
"Jianan Li,Keisuke Yanagisawa,Masatake Sugita,Takuya Fujie,Masahito Ohue,Yutaka Akiyama","CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides",,"Journal of Chemical Information and Modeling","American Chemical Society","Volume 63","Issue 7","pp. 2240-2250",2023,Mar.
"Masatake Sugita,Takuya Fujie,Keisuke Yanagisawa,Masahito Ohue,Yutaka Akiyama","Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations",,"Journal of Chemical Information and Modeling","American Chemical Society","Volume 62","Issue 18","pp. 4549-4560",2022,Sept.
"Keisuke Yanagisawa,Rikuto Kubota,Yasushi Yoshikawa,Masahito Ohue,Yutaka Akiyama","Effective Protein-Ligand Docking Strategy via Fragment Reuse and a Proof-of-Concept Implementation",,"ACS Omega","American Chemical Society","Volume 7","Issue 34","pp. 30265-30274",2022,Aug.
"能祖雄大,杉田昌岳,藤江拓哉,柳澤渓甫,大上雅史,秋山泰","分子動力学シミュレーション軌跡データからの環状ペプチドの膜透過性と相関が高い特徴量の抽出",,"研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-70","  50","  1-8",2022,June
"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.
"山崎眞拓,伊澤和輝,平田稜,柳澤渓甫,大上雅史,秋山泰","結合エネルギーを考慮したゲノムワイドな高速短鎖核酸配列検索手法の開発",,"研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-69","  8","  1-8",2022,Mar.
"稲垣雅也,柳澤渓甫,大上雅史,秋山泰","フラグメント化された化合物立体構造データベースの構築",,"研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-69","  15","  1-8",2022,Mar.
"津嶋佑旗,柳澤渓甫,大上雅史,秋山泰","新たなデータセットによる長距離フラグメントリンキング手法の再評価",,"研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-69","  16","  1-8",2022,Mar.
"玉野史結,伊澤和輝,柳澤渓甫,大上雅史,秋山泰","Gapmer型ASOにおけるオフターゲット効果のリスク評価手法の提案",,"研究報告バイオ情報学（BIO）","情報処理学会","  2022-BIO-69","  7","  1-7",2022,Mar.
"Jianan Li,Yanagisawa K,Yoshikawa Y,Ohue M,Akiyama Y.","Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning",,"Bioinformatics",,"Volume 38","Issue 4","  1110-1117",2022,Feb.
"Takabatake K,Yanagisawa K,Akiyama Y.","Solving Generalized Polyomino Puzzles Using the Ising Model",,"Entropy","MDPI","Vol. 24","Issue (3)","pp. 354",2022,Feb.
"杉田昌岳,杉山聡,藤江拓哉,吉川寧,柳澤渓甫,大上雅史,秋山泰","分子動力学シミュレーションに基づいた環状ペプチドの膜透過率の大規模予測","第58回日本生物物理学会年会",,,,,,2021,Nov.
"杉田昌岳,杉山聡,藤江拓哉,吉川寧,柳澤渓甫,大上雅史,秋山泰","分子動力学シミュレーションに基づいた環状ペプチドの膜透過率の大規模予測","第58回日本生物物理学会年会",,,,,,2021,Nov.
"杉田昌岳,杉山聡,藤江拓哉,吉川寧,柳澤渓甫,大上雅史,秋山泰","分子動力学シミュレーションに基づいた環状ペプチドの膜透過率の大規模予測","第43回溶液化学シンポジウム",,,,,,2021,Oct.
"Kazuki Takabatake,Kazuki Izawa,Motohiro Akikawa,Keisuke Yanagisawa,Masahito Ohue,Yutaka Akiyama","Improved Homology Search for Metagenomic Analysis by Two-Step Seed Search with Reduced Amino Acid Alphabets","The 10th International Conference on Bioinformatics and Biomedical Science (ICBBS2021)",,,,,,2021,Oct.
"Sugita M,Sugiyama S,Takuya Fujie,Yoshikawa Y,Yanagisawa K,Ohue M,Akiyama Y.","Large-scale membrane permeability prediction of cyclic peptides crossing a lipid bilayer based on enhanced sampling molecular dynamics simulations","CBI学会2021年大会",,,,,,2021,Oct.
"Takabatake K,Izawa K,Akikawa M,Yanagisawa K,Ohue M,Akiyama Y.","Improved large-scale homology search by two-step seed search using multiple reduced amino acid alphabets",,"Genes",,"  12","  9","  1455",2021,Sept.
"柳澤渓甫","タンパク質立体構造情報を用いた薬剤バーチャルスクリーニング",,"JSBi Bioinformatics Review","特定非営利活動法人日本バイオインフォマティクス学会","Volume 2","Issue 1","pp. 76-86",2021,Sept.
"津嶋佑旗,柳澤渓甫,大上雅史,秋山泰.","タンパク質表面との結合親和性を考慮した長距離フラグメントリンキング手法の開発","第67回BIO研究発表会","研究報告バイオ情報学（BIO）","情報処理学会","  2021-BIO-67","  1","Page 1-8",2021,Sept.
"Sugita M,Sugiyama S,Takuya Fujie,Yoshikawa Y,Yanagisawa K,Ohue M,Akiyama Y.","Large-scale membrane permeability prediction of cyclic peptides crossing a lipid bilayer based on enhanced sampling molecular dynamics simulations",,"Journal of Chemical Information and Modeling",,"  61","  7","  3681-3695",2021,July
"Isawa Kazuya,Yanagisawa Keisuke,Ohue Masahito,Akiyama Yutaka","Antisense oligonucleotide activity analysis based on opening and binding energies to targets","Proceedings of The 27th International Conference on Parallel & Distributed Processing Techniques and Applications (PDPTA’21)","Advances in Parallel & Distributed Processing and Applications",,,,,2021,July
"Keisuke Yanagisawa,Yoshitaka Moriwaki,Tohru Terada,Kentaro Shimizu","EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation",,,,"  61","  6","  2744-2753",2021,June
"井澤和也,柳澤渓甫,大上雅史,秋山泰","標的配列との結合・開放エネルギー推定に基づくアンチセンス核酸の阻害活性モデルの研究",,"情報処理学会研究報告",,"Vol. 2021-BIO-65","No. 7","pp. 1-7",2021,Mar.
"柳澤 渓甫","共溶媒分子動力学シミュレーションにおける創薬向け共溶媒セットの構築","第43回日本分子生物学会年会 (MBSJ2020)",,,,,,2020,Dec.
"久保田陸人,柳澤渓甫,吉川寧,大上雅史,秋山泰","共通な部分構造の再利用による高速なタンパク質リガンドドッキング手法の開発",,"情報処理学会研究報告",,"Vol. 2020-BIO-61","No. 4","pp. 1-8",2020,Mar.
"Keisuke Yanagisawa,Yoshitaka Moriwaki,Tohru Terada,Kentaro Shimizu","Systematic construction of the cosolvents sets for cosolvent MD (CMD) with the large-scale simulation","AHeDD2019/IPAB2019 Joint Symposium",,,,,,2019,Nov.
"Ohue M,Ii R,Yanagisawa K,Akiyama Y.","Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph","Parallel and Distributed Processing Techniques and Applications （PDPTA'19）","In Proceedings of the 2019 International Conference on Parallel and Distributed Processing Techniques & Applications (PDPTA'19)",,,,"Page 122-128",2019,July
"Ohue M,Ii R,Yanagisawa K,Akiyama Y.","Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph",,"IPSJ SIG Technical Report",,"Vol. 2019-MPS-124","No. 3","pp. 1-4",2019,July
"柳澤渓甫","化合物群の部分構造の共通性に着目した高速バーチャルスクリーニング手法の開発",,,,,,,2019,Mar.
"Keisuke Yanagisawa","Fast structure-based virtual screening with commonality of compound substructure",,,,,,,2019,Mar.
"Masahito Ohue,Takanori Hayashi,Yuri Matsuzaki,Keisuke Yanagisawa,Yutaka Akiyama","Megadock-Web: An Integrated Database of High-Throughput Structure-Based Protein-Protein Interaction Predictions","Biophysical Society 63rd Annual Meeting",,,,,,2019,Mar.
"Keisuke Yanagisawa","Fast structure-based virtual screening with commonality of compound substructure",,,,,,,2019,Mar.
"伊井 良太,柳澤 渓甫,大上 雅史,秋山 泰","分子グラフ上の距離を考慮したグラフ畳込みニューラルネットワークによる化合物活性予測","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","Vol. 2019-BIO-57","No. 11","pp. 1-8",2019,Mar.
"Takashi Tajimi,Naoki Wakui,Keisuke Yanagisawa,Yasushi Yoshikawa,Masahito Ohue,Yutaka Akiyama","Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques","the 29th International Conference on Genome Informatics (GIW 2018)","BMC Bioinformatics","Springer Nature","Volume 19",,,2018,Dec.
"Takashi Tajimi,Naoki Wakui,Keisuke Yanagisawa,Yasushi Yoshikawa,Masahito Ohue,Yutaka Akiyama","Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques",,"BMC Bioinformatics","Springer Nature","Volume 19",,,2018,Dec.
"Masahiro Mochizuki,Shogo Suzuki,Yanagisawa K,Ohue M,Akiyama Y.","QEX: target-specific druglikeness filter enhances ligand-based virtual screening",,"Molecular Diversity","Springer","Volume 23","issue 1","pp. 11-18",2018,July
"久保田陸人,柳澤渓甫,大上雅史,秋山泰","共通な部分構造の再利用アルゴリズムを用いたタンパク質リガンドドッキング手法の開発","情報処理学会研究報告 バイオ情報学（BIO）","研究報告バイオ情報学（BIO）","情報処理学会","  2018-BIO-54(42)",,"  1-8",2018,June
"Yanagisawa K,Komine S,Kubota R,Ohue M,Akiyama Y.","Optimization of memory use of fragment extension-based protein?ligand docking with an original fast minimum cost flow algorithm",,"Computational Biology and Chemistry (In Proc. APBC2018)",,"Volume 74",,"Page 399-406",2018,June
"Hayashi T,Matsuzaki Y,Yanagisawa K,Ohue M,Akiyama Y.","MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions",,"BMC Bioinformatics (In Proc. APBC2018)",,"  19","  (Suppl 4)","  62",2018,May
"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.
"柳澤渓甫,小峰駿汰,久保田陸人,大上雅史,秋山泰","フラグメント伸長型化合物ドッキング計算のための重み付きオフラインキャッシュ問題の厳密解アルゴリズム","情報処理学会 第50回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2017-BIO-50","  38","  1-8",2017,June
"柳澤渓甫,大上雅史,石田貴士,秋山泰","標的タンパク質の立体構造を用いたリガンド候補化合物の上限サイズの推定による化合物フィルタリング","情報処理学会 第49回バイオ情報学研究会","研究報告バイオ情報学（BIO）",,"  2017-BIO-49","  6","  1-7",2017,Mar.
"Yanagisawa K,Komine S,Shogo Suzuki,Ohue M,Ishida T,Akiyama Y.","Spresso: an ultrafast compound pre-screening method based on compound decomposition",,"Bioinformatics","OXFORD Academic","Volume 33","Issue 23","Page 3836-3843",2017,Mar.
"Keisuke Yanagisawa,Shunta Komine,Shogo Suzuki,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","ESPRESSO: An ultrafast compound pre-screening method with segmented compounds","Chem-Bio Informatics Society(CBI) Annual Meeting 2016",,,,,,2016,Oct.
"Keisuke Yanagisawa,Shunta Komine,Shogo Suzuki,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","ESPRESSO: An ultrafast compound pre-screening method based on compound decomposition","The 27th International Conference on Genome Informatics (GIW 2016)",,,,,,2016,Oct.
"Keisuke Yanagisawa,Shunta Komine,Shogo Suzuki,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","ESPRESSO: An ultrafast compound pre-screening method based on compound segmentation","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"柳澤 渓甫,小峰 駿汰,鈴木 翔吾,大上 雅史,石田 貴士,秋山 泰","フラグメント分割に基づく超高速化合物プレスクリーニング手法ESPRESSO","情報処理学会 第46回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2016-BIO-46","  18","  1-7",2016,June
"Keisuke Yanagisawa,Shunta Komine,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","Fast pre-filtering for virtual screening based on compound fragmentation","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.
"柳澤 渓甫,小峰 駿汰,大上 雅史,石田 貴士,秋山 泰","Fast pre-filtering for virtual screening based on ligand decomposition","第21回創剤フォーラム若手研究会",,,,,,2015,Nov.
"Keisuke Yanagisawa,Shunta Komine,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","Fast pre-filtering for virtual screening based on compound decomposition","IIBMP2015",,,,,,2015,Oct.
"Keisuke Yanagisawa,Takashi Ishida,Yutaka Akiyama","Drug Clearance Pathway Prediction Based on Semi-supervised Learning",,"IPSJ Transactions on Bioinformatics",,"Vol. 8",,"pp. 21-27",2015,Aug.
"鈴木翔吾,柳澤渓甫,大上雅史,石田貴士,秋山泰","SVMとDeep Learningに基づくヒトc-Yesキナーゼ阻害化合物の予測","情報処理学会 第42回バイオ情報学研究会","研究報告バイオ情報学（BIO）","情報処理学会","  2015-BIO-42","  36","  1-7",2015,June