"Guillaume Launay,Masahito Ohue,Julia Prieto Santero,Yuri Matsuzaki,C?cile Hilpert,Nobuyuki Uchikoga,Takanori Hayashi,Juliette Martin","Evaluation of CONSRANK-like scoring functions for rescoring ensembles of protein-protein docking poses",,"Frontiers in Molecular Biosciences",,"vol. 7",,,2020,Oct.
"Kento Aoyama,Masanori Kakuta,Yuri Matsuzaki,Takashi Ishida,Masahito Ohue,Yutaka Akiyama","Development of computational pipeline software for genome/exome analysis on the K computer",,"Supercomputing Frontiers and Innovations",,"Vol. 7","No. 1","pp. 37-54",2020,
"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.
"Nobuyuki Uchikoga,Yuri Matsuzaki","Analysis of amino acid sequences of protein interaction surfaces by rigid-body docking for known and unknown protein complex pairs.",,,,,,,2018,Sept.
"Masahito Ohue,Takanori Hayashi,Hiroki Watanabe,Yuri Matsuzaki,Nobuyuki Uchikoga,Yutaka Akiyama","Supercomputing-based exhaustive protein-protein interaction prediction and its open database.","The 56th Annual Meeting of the Biophysical Society of Japan",,,,,,2018,Sept.
"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
"林孝紀,山本悠生,松崎由理,大上雅史,秋山泰","タンパク質間相互作用予測統合データベースMEGADOCK-WEBの改良とクラウド計算環境との連携","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","  39","  1-8",2017,June
"Yuri Matsuzaki,Nobuyuki Uchikoga,Masahito Ohue,Yutaka Akiyama","Rigid-Docking Approaches to Explore Protein?Protein Interaction Space",,"Advances in Biochemical Engineering/Biotechnology(Network Biology)","Springer, Cham","volume 160",,"pp. 33-35",2017,May
"Yuri Matsuzaki,Simm, Jaak,Uchikoga, Nobuyuki,Yutaka Akiyama","A Docking Based Approach to Analyze Interaction Surfaces of Virus-Host Protein-Protein Interactions","58th Annual Meeting of the Biophysical-Society","BIOPHYSICAL JOURNAL","CELL PRESS","Vol. 112","No. 3","pp. 451A-452A",2017,Feb.
"Masahito Ohue,Yamamoto, Yuki,Hayashi, Takanori,Yuri Matsuzaki,Yutaka Akiyama","Cloud Computing for All-To-All Protein-Protein Docking on Azure HPC","58th Annual Meeting of the Biophysical-Society","BIOPHYSICAL JOURNAL","CELL PRESS","Vol. 112","No. 3","pp. 451A-451A",2017,Feb.
"Uchikoga, Nobuyuki,Yuri Matsuzaki,Masahito Ohue,Yutaka Akiyama","Interaction Surfaces of Proteins Involved in Bacterial Chemotaxis with Rigid-Body Docking Decoys","58th Annual Meeting of the Biophysical-Society","BIOPHYSICAL JOURNAL","CELL PRESS","Vol. 112","No. 3","pp. 290A-290A",2017,Feb.
"Takanori Hayashi,Kazuki Nagasawa,Yuri Matsuzaki,Masahito Ohue,Yutaka Akiyama","MEGADOCK-WEB: a database of predicted protein-protein interactions and its web interface","Informatics in Biology, Medicine and Pharmacology 2016 (IIBMP2016)",,,,,,2016,Sept.
"Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue,Yutaka Akiyama","Specificity of broad protein interaction surfaces for proteins with multiple binding partners",,"Biophysics and Physicobiology","THE BIOPHYSICAL SOCIETY OF JAPAN","Vol. 13",,"pp. 105-115",2016,July
"青山 健人,角田 将典,松崎 由理,石田 貴士,秋山 泰","スーパーコンピュータ「京」上でのエクソーム解析パイプラインの開発",,"情報処理学会論文誌コンピューティングシステム（ACS）",,"Vol. 9","No. 2","p. 15-33",2016,July
"内古閑伸之,松崎由理,大上雅史,秋山泰","細菌走化性におけるタンパク質間相互作用面の解析","第16回日本蛋白質科学会年会",,,,,,2016,June
"長澤一輝,松崎由理,大上雅史,秋山泰","タンパク質間相互作用予測結果データベース及び表示系の構築","情報処理学会 第45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-45","  2","  1-4",2016,Mar.
"Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue,Yutaka Akiyama","Analysis of Physico-Chemical Properties of Protein Docking Decoys Generated by Rigid-Body Docking","Biophysical Society 60th Annual Meeting",,,,,,2016,Feb.
"Yuri Matsuzaki,Simm, Jaak","Rigid Docking Based Protein-Protein Interaction Prediction using High Scoring Docking Models","60th Annual Meeting of the Biophysical-Society","BIOPHYSICAL JOURNAL","CELL PRESS","Vol. 110","No. 3","pp. 327A-327A",2016,Feb.
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers","Biophysical Society 60th Annual Meeting",,,,,,2016,Feb.
"大上雅史,松崎由理,石田貴士,秋山泰","タンパク質間相互作用予測システムMEGADOCKによるEGFRパスウェイ解析","第21回創剤フォーラム若手研究会",,,,,,2015,Nov.
"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.
"Yuri Matsuzaki,Masahito Ohue,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK: A high-performance protein-protein interaction prediction software for petascale supercomputing environments","3nd IIT Madras ? Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics",,,,,,2015,Nov.
"Uchikoga, Nobuyuki,Masahito Ohue,Yuri Matsuzaki,Yutaka Akiyama","Post-docking analysis by physicochemical properties of protein-protein interactions generated from rigid-body docking processes","29th Annual Symposium of the Protein-Society","PROTEIN SCIENCE","WILEY-BLACKWELL","Vol. 24",,"pp. 253-253",2015,Oct.
"内古閑伸之,松崎由理,大上雅史,秋山泰","剛体アンサンブルドッキングによって得られた候補構造群における相互作用残基ペアの特徴の解析","第53回日本生物物理学会年会",,,,,,2015,Sept.
"大上雅史,内古閑伸之,松崎由理,秋山泰","アミノ酸プロファイルによるタンパク質ペプチド複合体のポストドッキング解析","第53回日本生物物理学会年会",,,,,,2015,Sept.
"大上雅史,内古閑伸之,松崎由理,秋山泰","タンパク質間相互作用残基の物理化学的性質による単純化プロファイルを用いたポストドッキング解析","第15回日本蛋白質科学会年会",,,,,,2015,June
"Yuri Matsuzaki,Nobuyuki Uchikoga,Masahito Ohue,Yutaka Akiyama","Prediction of human-virus protein-protein interactions by exhaustive rigid docking.","Biophysical Society 59th Annual Meeting",,,,,,2015,Feb.
"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.
"Masahito Ohue,Takehiro Shimoda,Shuji suzuki,Yuri Matsuzaki,Takashi Ishida,Yutaka Akiyama","MEGADOCK 4.0: an ultra?high-performance protein-protein docking software for heterogeneous supercomputers","APBC 2015: The Thirteenth Asia Pacific Bioinformatics Conference",,,,,,2015,Jan.
"Masahito Ohue,Takehiro Shimoda,Shuji suzuki,Yuri Matsuzaki,Takashi Ishida,Yutaka Akiyama","MEGADOCK 4.0: an ultra?high-performance protein-protein docking software for heterogeneous supercomputers","GIW/ISCB-Asia 2014",,,,,,2014,Dec.
"Masahito Ohue,Takehiro Shimoda,Shuji Suzuki,Yuri Matsuzaki,Takashi Ishida,Yutaka Akiyama","The MEGADOCK Project: high-performance protein-protein interaction prediction tools on supercomputing environments","The Asia hub for e-drug discovery symposium 2014 (AHeDD' 2014)",,,,,,2014,Nov.
"Masahito Ohue,Takehiro Shimoda,Shuji Suzuki,Yuri Matsuzaki,Takashi Ishida,Yutaka Akiyama","MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers","IIBMP2014","Bioinformatics",,"Volume 30","Issue 22","page 3281-3283",2014,Nov.
"大上雅史,松崎由理,石田貴士,秋山泰","タンパク質とペプチドのドッキング計算","生命情報科学若手の会 第6回研究会",,,,,,2014,Oct.
"内古閑伸之,松崎由理,大上雅史,広川貴次,秋山泰","Analysis of properties of protein-protein interaction surface areas involved in more near-native conmplexes by Re-docking scheme","第52回日本生物物理学会年会",,,,,,2014,Sept.
"Masahito Ohue,Takehiro Shimoda,Shuji Suzuki,Yuri Matsuzaki,Takashi Ishida,Yutaka Akiyama","The MEGADOCK Project: high-performance protein-protein interaction prediction tools on supercomputing environments","Biophysical Society Thematic Meeting Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations",,,,,,2014,Sept.
"大上雅史,松崎由理,内古閑伸之,石田貴士,秋山泰","MEGADOCK: a high-performance protein-protein interaction prediction tool on supercomputing environments","第52回日本生物物理学会年会",,,,,,2014,Sept.
"Ohue, M.,Shimoda, T.,Suzuki, S.,Matsuzaki, Y.,Ishida, T.,Akiyama, Y.","MEGADOCK 4.0: an ultra?high-performance protein?protein docking software for heterogeneous supercomputers",,"Bioinformatics","Oxford University Press","Vol. 30","No. 22","pp. 3281-3283",2014,Aug.
"大上 雅史,下田 雄大,松崎由理,石田 貴士,秋山泰","大規模GPUクラスタによるタンパク質ドッキング計算システム",,"研究報告数理モデル化と問題解決（MPS）","一般社団法人情報処理学会","Vol. 2014","No. 32","pp. 1-4",2014,June
"大上 雅史,下田 雄大,松崎由理,石田 貴士,秋山泰","大規模GPUクラスタによるタンパク質ドッキング計算システム (情報論的学習理論と機械学習)",,"電子情報通信学会技術研究報告 = IEICE technical report : 信学技報","一般社団法人電子情報通信学会","Vol. 114","No. 105","pp. 173-176",2014,June
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK: An all-to-all protein-protein interaction prediction system using tertiary structure data",,"Protein and Peptide Letters","Bentham Science","Volume 21","Issue 8","Page 766-778",2014,June
"青山 健人,角田 将典,松崎 由理,石田 貴士,秋山 泰","エクソーム解析パイプラインの京コンピュータ上での大規模並列化","情報処理学会第38回バイオ情報学研究会","情報処理学会研究報告",,"  2014-BIO-38",,,2014,June
"大上 雅史,下田 雄大,松崎由理,石田貴士,秋山泰","大規模GPUクラスタによるタンパク質ドッキング計算システム (ニューロコンピューティング)",,"電子情報通信学会技術研究報告 = IEICE technical report : 信学技報","一般社団法人電子情報通信学会","Vol. 114","No. 104","pp. 173-176",2014,June
"大上雅史,下田 雄大,松崎由理,石田貴士,秋山泰","大規模GPUクラスタによるタンパク質ドッキング計算システム",,"研究報告バイオ情報学（BIO）","一般社団法人情報処理学会","Vol. 2014-BIO-38","No. 32","pp. 1-4",2014,June
"大上雅史,下田雄大,松崎由理,内古閑伸之,鈴木脩司,石田貴士,秋山泰","MEGADOCK 4.0: mega-dock per dayへの道のり",,"生命情報科学若手の会 第5回研究会",,,,,2014,Feb.
"Yuri Matsuzaki,Nobuyuki Uchikoga,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","Prediction of protein-protein interactions based on tertiary structures and transcription information","Biophysical Society 58th Annual Meeting",,,,,,2014,Feb.
"Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue,Takatsugu Hirokawa,Yutaka Akiyama","Re-docking scheme to explore docking search space by using interaction profiles","Biophysical Society 58th Annual Meeting",,,,,,2014,Feb.
"Masahito Ohue,Yuri Matsuzaki,Takehiro Shimoda,Takashi Ishida,Yutaka Akiyama","Highly Precise Protein-Protein Interaction Prediction Based on Consensus Between Template-Based and de Novo Docking Methods",,"BMC Proceedings","BioMed Central","Volume 7","  Supplement 7","  S6",2013,Dec.
"Masahito Ohue,Yuri Matsuzaki,Takehiro Shimoda,Takashi Ishida,Yutaka Akiyama","Highly precise protein-protein interaction prediction by integrating template-based and template-free protein docking","The 2013 Annual Conference of the Japanese Society for Bioinformatics (JSBi2013)",,,,,"  P077",2013,Nov.
"Masahito Ohue,Yuri Matsuzaki,Takehiro Shimoda,Takashi Ishida,Yutaka Akiyama","Highly precise protein-protein interaction prediction by integrating template-based and template-free protein docking","2nd IIT Madras ? Tokyo Tech Joint Symposium on Techniques and Applications of Bioinformatics",,,,,"  P08",2013,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.
"Takehiro Shimoda,Masahito Ohue,Yuri Matsuzaki,Takayuki Fujiwara,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","The MEGADOCK project: Ultra-high-performance protein-protein interaction prediction tools on supercomputing environments","ACM Conference on Bioinformatics, Computatioal Biology and Biomedical Informatics (ACM-BCB2013)",,,,,"p. 668",2013,Sept.
"Masahito Ohue,Yuri Matsuzaki,Takehiro Shimoda,Takashi Ishida,Yutaka Akiyama","Improvement of protein-protein interaction prediction by integrating template-based and template-free protein docking","ACM Conference on Bioinformatics, Computatioal Biology and Biomedical Informatics (ACM-BCB2013)",,,,,"p. 667",2013,Sept.
"Yuri Matsuzaki,Masahito Ohue,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","Structure based protein-protein interaction network prediction of EGFR signaling related proteins using MEGADOCK","2nd IIT Madras ? Tokyo Tech Joint Symposium on Techniques and Applications of Bioinformatics",,,,,,2013,Sept.
"Yuri Matsuzaki,Nobuyuki Uchikoga,Masahito Ohue,Takehiro Shimoda,Toshiyuki Sato,Takashi Ishida,Yutaka Akiyama","MEGADOCK 3.0: A high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments",,"Source Code for Biology and Medicine","BioMed Central","Vol. 8","No. 1",,2013,Sept.
"Nobuyuki Uchikoga,Yuri Matsuzaki,Masahito Ohue,Takatsugu Hirokawa,Yutaka Akiyama","Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints",,"PLOS ONE",,"Vol. 8","No. 7","  e69365",2013,July
"Yuri Matsuzaki,Masahito Ohue,Nobuyuki Uchikoga,Yutaka Akiyama","Protein-protein interaction network prediction by using rigid-body docking tools: application to bacterial chemotaxis",,"Protein and Peptide Letters","Bentham Science","Volume 21","Issue 8","pp. 790-798",2013,July
"大上雅史,松崎由理,内古閑伸之,石田貴士,秋山泰","MEGADOCK：構造ドッキング計算を用いたタンパク質間相互作用の大規模予測",,"第13回日本蛋白質科学会年会",,,,"  1P-059",2013,June
"Masahito Ohue,Yuri Matsuzaki,Takehiro Shimoda,Takashi Ishida,Yutaka Akiyama","Highly Precise Protein-Protein Interaction Prediction Based on Consensus Between Template-Based and de Novo Docking Methods","Great Lakes Bioinformatics Conference 2013","Proceedings of Great Lakes Bioinformatics Conference 2013",,,,"pp. 100-109",2013,May
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Kohei Yamamoto,Takayuki Fujiwara,Takehiro Shimoda,Toshiyuki Sato,Takashi Ishida,Yutaka Akiyama","Protein-protein interaction prediction based on rigid-body docking with ultra-high-performance computing technique: applications to affinity prediction on CAPRI round 21 and interactome analyses",,"CAPRI 2013 5th Evaluation Meeting",,,,,2013,Apr.
"大上雅史,松崎由理,内古閑伸之,山本航平,下田雄大,藤原隆之,石田貴士,秋山泰","MEGADOCK 3.0：超並列タンパク質間相互作用予測システム",,"生命情報科学若手の会 第4回研究会",,,,,2013,Mar.
"秋山泰,松崎由理,石田貴士,大上雅史,内古閑 伸之","網羅的タンパク質ドッキング予測プログラムMEGADOCKの開発と応用","文部科学省「革新的ハイパフォーマンス・コンピューティング・インフラ （HPCI） の構築」HPCI戦略プログラム「グランドチャレンジ・アプリケーションの研究開発」公開シンポジウム",,,,,,2013,Mar.
"松崎由理,大上雅史,石田貴士,内古閑伸之,秋山泰","大規模タンパク質間ネットワーク推定に関する研究","平成24年度「京」を中核とするHPCIシステム利用研究課題中間報告会",,,,,,2013,Mar.
"Yuri Matsuzaki,Nobuyuki Uchikoga,Masahito Ohue,Takashi Ishida,Yutaka Akiyama","Protein-protein interaction network prediction by using rigid-body docking tool MEGADOCK","Biophysical Society 57th Annual Meeting",,,,,,2013,Feb.
"大上雅史,松崎由理,石田貴士,秋山泰","MEGADOCK: 大規模タンパク質間相互作用予測システムとその応用","HPCS2013 ハイパフォーマンスコンピューティングと計算科学シンポジウム",,,,,,2013,Jan.
"秋山泰,松崎由理,大上雅史,石田貴士,内古閑伸之","網羅的タンパク質ドッキング解析プログラムMEGADOCKの開発と応用","ISLiMソフトウェア研究開発報告会",,,,,,2013,Jan.
"Yuri Matsuzaki,Masahito Ohue,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","Application of exhaustive protein-protein interaction prediction system by using protein docking to signal transduction pathways.","International Society for Computational Biology, ISCB-Asia 2012",,,,,,2012,Dec.
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK: A rapid screening system of protein-protein interactions with all-to-all physical docking.","International Society for Computational Biology, ISCB-Asia 2012",,,,,,2012,Dec.
"大上雅史,松崎由理,石田貴士,秋山泰","MEGADOCKを用いたタンパク質間相互作用予測のヒトアポトーシスパスウェイ解析への応用","第32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","Vol. 2012-BIO-32","No. 13","pp. 1-8",2012,Nov.
"Masahito Ohue,Yuri Matsuzaki,Takashi Ishida,Yutaka Akiyama","Improvement of the protein-protein docking prediction by introducing a simple hydrophobic interaction model: an application to interaction pathway analysis.","The 7th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB2012)","Lecture Notes in Bioinformatics","Springer Heidelberg","Vol. 7632",,"Page 178-187",2012,Nov.
"Yuri Matsuzaki,Masahito Ohue,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","Application of exhaustive protein-protein interaction prediction system by using protein docking to signal transduction pathways.","20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2012)",,,,,,2012,July
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK: A rapid screening system of protein-protein interactions with all-to-all physical docking.","3DSIG: The 8th structural bioinformatics and computational biophysics meeting",,,,,,2012,July
"Yuri Matsuzaki,Masahito Ohue,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","Application of exhaustive protein-protein interaction prediction system by using protein docking to signal transduction pathways.","3DSIG: The 8th structural bioinformatics and computational biophysics meeting",,,,,,2012,July
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK: A rapid screening system of protein-protein interactions with all-to-all physical docking.","20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2012)",,,,,,2012,July
"藤原 隆之,松崎由理,石田貴士,秋山泰","タンパク質間ドッキング予測における目的関数の機械学習を用いた動的調整",,"電子情報通信学会技術研究報告. NC, ニューロコンピューティング","一般社団法人電子情報通信学会","Vol. 112","No. 108","pp. 101-103",2012,June
"藤原隆之,松崎由理,石田貴士,秋山泰","タンパク質間ドッキング予測における機械学習を用いた目的関数の動的調整","第29回バイオ情報学研究会","情報処理学会研究報告",,"Vol. 2012-BIO-29","No. 19","pp. 1-3",2012,June
"松崎 由理,内古閑 伸之,大上 雅史,秋山 泰","網羅的タンパク質ドッキング解析プログラムMEGADOCKの開発と応用","文部科学省「革新的ハイパフォーマンス・コンピューティング・インフラ（HPCI）の構築」（※1） 次世代ナノ統合シミュレーションソフトウェアの研究開発（ナノ）（※2） 次世代生命体統合シミュレーションソフトウェアの研究開発（ライフ） 公開シンポジウム",,,,,,2012,Mar.
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","Protein Complex Structure Prediction with Normal Mode Ensemble and Physical Docking","Bioinformatics week in Odaiba 2011 (BiWO2011)","Bioinformatics week in Odaiba 2011 (BiWO2011)",,,,"  P-01",2012,Jan.
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","Bound state structure estimation of protein-protein complex using rigid-body protein-protein docking method","The 10th Asia-Pacific Bioinformatics Conference (APBC2012)","The 10th Asia-Pacific Bioinformatics Conference (APBC2012)",,,,"  P-50",2012,Jan.
"秋山 泰,松崎 由理,内古閑 伸之,石田 貴士,大上 雅史","網羅的タンパク質ドッキング解析プログラムMEGADOCKの開発と応用","次世代生命体統合シミュレーションソフトウェアの研究開発成果報告会 ISLiM成果報告会2011",,,,,,2011,Dec.
"Masahito Ohue,Yuri Matsuzaki,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","Binding Conformation Prediction of a Protein Complex Using Physical Docking","GCOE Compview Final Symposium (Preliminary event of ISAAC 2011)",,,,,,2011,Dec.
"Sarel J. Fleishman,Timothy A. Whitehead,Eva-Maria Strauch,Jacob E. Corn,Sanbo Qin,Huan-Xiang Zhou,Julie C. Mitchell,Omar N. A. Demerdash,Mayuko Takeda-Shitaka,Genki Terashi,Iain H. Moal,Xiaofan Li,Paul A. Bates,Martin Zacharias,Hahnbeom Park,Jun-su Ko,Hasup Lee,Chaok Seok,Thomas Bourquard,Julie Bernauer,Anne Poupon,Jerome Aze,Seren Soner,Sefik Kerem Oval.,Pemra Ozbek,Nir Ben Tal,Turkan Haliloglu,Howook Hwang,Thom Vreven,Brian G. Pierce,Zhiping Weng,Laura Perez-Cano,Carles Pons,Juan Fernandez-Recio,Fan Jiang,Feng Yang,Xinqi Gong,Libin Cao,Xianjin Xu,Bin Liu,Panwen Wang,Chunhua Li,Cunxin Wang,Charles H. Robert,Mainak Guharoy,Shiyong Liu,Yangyu Huang,Lin Li,Dachuan Guo,Ying Chen,Yi Xiao,Nir London,Zohar Itzhaki,Ora Schueler-Furman,Yuval Inbar,Vladimir Patapov,Mati Cohen,Gideon Schreiber,Yuko Tsuchiya,Eiji Kanamori,Daron M. Standley,Haruki Nakamura,Kengo Kinoshita,Camden M. Driggers,Robert G. Hall,Jessica L. Morgan,Victor L. Hsu,Jian Zhan,Yuedong Yang,Yaoqi Zhou,Panagiotis L. Kastritis,Alexandre M. J. J. Bonvin,Weiyi Zhang,Carlos J. Camacho,Krishna P. Kilambi,Aroop Sircar,Jeffrey J. Gray,Masahito Ohue,Nobuyuki Uchikoga,Yuri Matsuzaki,Takashi Ishida,Yutaka Akiyama,Raed Khashan,Stephen Bush,Denis Fouches,Alexander Tropsha,Juan Esquivel-Rodriguez,Daisuke Kihara,P. Benjamin Stranges,Ron Jacak,Brian Kuhlman,Sheng-You Huang,Xiaoqin Zou,Shoshana J. Wodak,Joel Janin,David Baker","Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology",,"Journal of Molecular Biology","ScienceDirect","Volume 414","Issue 2","pp. 289-302",2011,Nov.
"内古閑 伸之,松崎 由理,大上 雅史,広川 貴次,秋山 泰","相互作用プロファイルを用いたタンパク質間ドッキングの代表相互作用の探索","第49回日本生物物理学会年会",,,,,,2011,Sept.
"Yuri Matsuzaki,Masahito Ohue,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK: a Fast Protein-protein Interaction Prediction System by Exhaustive Docking","12th International Conference on Systems Biology (ICSB 2011)",,,,,,2011,Sept.
"松崎由理,内古閑伸之,大上雅史,石田貴士,秋山泰","MEGADOCK: 網羅的な立体構造のドッキングによるタンパク質間相互作用予測アプリケーション","バイオスーパーコンピューティング サマースクール2011バイオスーパーコンピューティング",,,,,,2011,Sept.
"Masahito Ohue,Yuri Matsuzaki,Yutaka Akiyama","Docking-calculation-based Method for Predicting Protein-RNA Interactions",,"Genome Informatics",,"Volume 25","Issue 1","pp. 25-39",2011,Aug.
"Yuri Matsuzaki,Masahito Ohue,Nobuyuki Uchikoga,Takashi Ishida,Yutaka Akiyama","MEGADOCK: A fast protein-protein interaction prediction system by exhaustive docking","The 9th International Workshop on Advanced Genomics",,,,,,2011,July
"山本航平,大上雅史,内古閑伸之,松崎由理,石田貴士,秋山 泰","タンパク質間相互作用予測における可視化手法の開発および予測精度の改善","情報処理学会 第25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","vol. 2011-BIO-25","  31","pp. 1-7",2011,June
"大上雅史,松崎由理,内古閑伸之,石田貴士,秋山 泰","ドッキング計算に基づく網羅的タンパク質-RNA間相互作用予測","情報処理学会 第25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","vol. 2011-BIO-25","  30","pp. 1-8",2011,June
"山本航平,大上雅史,松崎由理,石田貴士,秋山 泰","タンパク質ドッキング計算結果の可視化とその解析","情報処理学会 第73回全国大会",,,,,,2011,Mar.
"大上雅史,松崎由理,秋山 泰","立体構造情報を用いたドッキング計算による大規模タンパク質-RNA間相互作用予測手法","情報処理学会 第73回全国大会",,,,,,2011,Mar.
"松崎由理,内古閑伸之,大上雅史,石田貴士,秋山泰","MEGADOCKを用いたタンパク質間相互作用予測のシグナル伝達系への応用","第3回 バイオスーパーコンピューティングシンポジウム",,,,,,2011,Feb.
"Matsuzaki Yuri.,Uchikoga Nobuyuki.,Ohue Masahito.,Ishida Takashi.,Akiyama Yutaka","Exhaustive protein-protein interaction prediction with MEGADOCK and its application to signaling pathway estimation","Asia Hub for e-Drug Discovery (AHeDD) Symoposium 2010",,,,,,2010,Dec.
"Masahito Ohue,Yuri Matsuzaki,Yutaka Akiyama","Development of a Protein-RNA Interaction Prediction Method Based on a Docking Calculation","The 2010 Annual Conference of the Japanese Society for Bioinformatics (JSBi2010)",,,,,,2010,Dec.
"Yutaka Akiyama,Yuri Matsuzaki,Nobuyuki Uchikoga,Masahito Ohue","Exhaustive protein-protein interaction network prediction by using MEGADOCK",,"BioSupercomputing Newsletter","Computational Science Research Program, RIKEN Research Cluster for Innovation","Vol. 3",,"pp. 8",2010,Dec.
"松崎由理,大上雅史,内古閑伸之,石田貴士,秋山 泰","MEGADOCKによるタンパク質間相互作用予測?システム生物学への応用?",,"TSUBAME e-Science Journal","東京工業大学 学術国際情報センター","vol. 2","No. 2","pp. 14-18",2010,Nov.
"Matsuzaki Yuri.,Ohue Masahito.,Matsuzaki Yusuke.,Sato Toshuyuki,Akiyama Yutaka","A computational screening system of protein-protein interactions: connecting protein structural information to biological pathway estimation","11th International Conference on Systems Biology (ICSB)",,,,,,2010,Oct.
"大上雅史,松崎由理,松崎裕介,佐藤智之,秋山泰","MEGADOCK：立体構造情報からの網羅的タンパク質間相互作用予測とそのシステム生物学への応用","情報処理学会数理モデル化と問題解決研究会","情報処理学会論文誌数理モデル化と応用（TOM）","情報処理学会","Vol. 3","No. 3","pp. 91-106",2010,Oct.
"Masahito Ohue,Yuri Matsuzaki,Yusuke Matsuzaki,Toshiyuki Sato,Yutaka Akiyama","n silico prediction of PPI network with structure-based all-to-all docking","InCoB2010 - the 9th International Conference on Bioinformatics",,,,,,2010,Sept.
"Yuri Matsuzaki","A computational screening system of protein-protein interactions: connecting protein structural information to biological pathway estimation","ETHZ - Tokyo Tech Workshop : Computing with GPUs, Cells, and Multicores",,,,,,2010,May
"大上雅史,松崎由理,松崎裕介,佐藤智之,秋山泰","MEGADOCK：立体構造情報からの網羅的タンパク質間相互作用予測とそのシステム生物学への応用","情報処理学会数理モデル化と問題解決研究会","研究報告数理モデル化と問題解決（MPS）","情報処理学会","Vol. 2010-MPS-78","No. 3","pp. 1-9",2010,May
"大上雅史,松崎裕介,松崎由理,佐藤智之,秋山 泰","エネルギー計算に基づくリランキングとクラスタリングを用いた網羅的タンパク質間相互作用予測手法の提案","第2回データ工学と情報マネジメントに関するフォーラム(DEIM2010)","第2回データ工学と情報マネジメントに関するフォーラム(DEIM2010)",,,"  E4-4",,2010,Mar.
"松崎由理","MEGADOCKの網羅的タンパク質相互作用予測への応用 （細菌走化性での評価、EGFRでの予備評価）","第１０回データ解析融合ワークショップ",,,,,,2010,Mar.
"Masahito Ohue,Yusuke Matsuzaki,Yuri Matsuzaki,Toshiyuki Sato,Yutaka Akiyama","MEGADOCK: An all-to-all protein-protein interaction prediction system -- Improving the accuracy using boosting and binding energy reranking.","The 2nd Biosupercomputing Symposium",,,,,,2010,Mar.
"Yuri Matsuzaki,Yusuke Matsuzaki,Masahito Ohue,Toshiyuki Sato,Yutaka Akiyama","A computational screening system of protein-protein interactions: connecting structural information to pathway estimation.","The 2nd Biosupercomputing Symposium",,,,,,2010,Mar.
"松崎裕介,大上雅史,松崎由理,佐藤智之,関嶋政和,秋山泰","タンパク質の特性に基づくunboundドッキングのための剛体予測手法の改良","情報処理学会 第20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","Vol. 2010-BIO-20","No. 4","pp. 1-8",2010,Feb.
"大上雅史,松崎裕介,松崎由理,佐藤智之,秋山泰","リランキングを用いたタンパク質ドッキングの精度向上と網羅的タンパク質間相互作用予測への応用","情報処理学会 第20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","Vol. 2010-BIO-20","No. 3","pp. 1-8",2010,Feb.
"Yuri Matsuzaki,Yusuke Matsuzaki,Toshiyuki Sato,Yutaka Akiyama","In silico screening of protein-protein interactions with all-to-all rigid docking and clustering: an application to pathway analysis",,"Journal of Bioinformatics and Computational Biology",,"Vol. 7","No. 6","  991-1012",2009,Dec.
"Masahito Ohue,Yusuke Matsuzaki,Yuri Matsuzaki,Yutaka Akiyama","Improvement of all-to-all protein-protein interaction prediction system MEGADOCK","The 20th International Conference on Genome Informatics Workshop(GIW2009)","The 20th International Conference on Genome Informatics Workshop Poster Proceedings",,,,"  P033",2009,Dec.
"Yuri Matsuzaki,Yusuke Matsuzaki,Masahito Ohue,Toshiyuki Sato,Yutaka Akiyama","A computational screening system of protein-protein interactions using tertiary structure data: an application to signaling pathway analysis.","BIOINFO 2009 CBI-KSBSB Joint Conference","Proc. BIOINFO 2009 CBI-KSBSB Joint Conference",,,,"  P11-114",2009,Nov.
"Yusuke Matsuzaki,Yuri Matsuzaki,Masakazu Sekijima,Yutaka Akiyama","Protein structure sampling based on molecular dynamics and improvement of docking prediction","BIOINFO 2009 CBI-KSBSB Joint Conference","Proc. BIOINFO 2009 CBI-KSBSB Joint Conference",,,,"  P10-99",2009,Nov.
"Masahito Ohue,Yusuke Matsuzaki,Yuri Matsuzaki,Yutaka Akiyama","Improvement of all-to-all protein-protein interaction prediction system MEGADOCK","BIOINFO 2009 CBI-KSBSB Joint Conference","Proc. BIOINFO 2009 CBI-KSBSB Joint Conference",,,,"  P10-101",2009,Nov.
"Takeshi Sakurada,Moriyoshi Koizumi,Sachio Nohara,Chihiro Okada,Yuri Matsuzaki,Masaru Tomita","E-Cell IDE: an integrated modelling and simulation environment for systems-biology","The 10th International Conference on Systems Biology (ICSB 2009)",,,,,,2009,Sept.
"Yuri Matsuzaki,Yusuke Matsuzaki,Masahito Ohue,Toshiyuki Sato,Yutaka Akiyama","In silico screening of protein-protein interactions with all-to-all rigid docking and clustering: an application to pathway analysis","The 10th International Conference on Systems Biology (ICSB 2009)",,,,,,2009,Sept.
"松崎裕介,松崎由理,関嶋政和,秋山泰","分子動力学法に基づくタンパク質構造サンプリングとドッキング予測の改良","情報処理学会 第18回バイオ情報学研究会","情報処理学会研究報告","情報処理学会","Vol. 2009-BIO-18,","No. 1","pp. 1-6",2009,Sept.
"大上雅史,松崎裕介,松崎由理,秋山泰","網羅的タンパク質間相互作用予測システムにおける判別精度の改良","情報処理学会 第18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","Vol. 2009-BIO-18","No. 3","pp. 1-8",2009,Sept.
"Yuri Matsuzaki,Yusuke Matsuzaki,Masahito Ohue,Toshiyuki Sato,Yutaka Akiyama","A computational screening system of protein-protein interactions using tertiary structure data: with application to pathway analysis","Joint Computational Science Workshop 2009",,,,,,2009,July
"大上雅史,松崎裕介,松崎由理,佐藤智之,秋山泰","物理化学的相互作用の導入による網羅的タンパク質間相互作用予測システムの高精度化","情報処理学会 第17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","  2009-BIO-17","  11","  1-8",2009,May
"松崎 由理,松崎 裕介,大上雅史,佐藤 智之,秋山 泰","ドッキング後処理によるPPI検出システムの応用と評価?EGFRシグナル伝達系への適用にむけて","第8回データ解析融合ワークショップ（公開ワークショップ）",,,,,,2009,Mar.
"松崎由理","形状相補性に基づくall-to-allドッキングによる網羅的なタンパク質間相互作用予測","平成20年度 第6回IPABオープンセミナー  
第6回IPABオープンセミナー「タンパク質構造解析の新潮流」",,,,,,2009,Mar.
"櫻田剛史,小泉守義,野原祥夫,岡田千尋,松崎由理,冨田勝","E-Cell IDE: システムバイオロジーのためのモデリング・シミュレーション統合環境",,"情報処理学会 研究報告",,"Vol. 2009","No. 25","pp. 25-28",2009,Feb.
"Yuri Matsuzaki,Yusuke Matsuzaki,Toshiyuki Sato,Yutaka Akiyama","Virtual screening of protein-protein interactions: an application to known signal transduction systems","The 2008 Annual Conference of the Japanese Society for Bioinformatics (JSBi2008)",,,,,,2008,Dec.
"Yutaka Akiyama,Toshiyuki Sato,Yusuke Matsuzaki,Yuri Matsuzaki","Megadock - a rapid screening system for all-to-all protein docking analysis with precalculated fourier library of protein structures","The 2008 Annual Conference of the Japanese Society for Bioinformatics (JSBi2008)",,,,,,2008,Dec.
"Yutaka Akiyama,Toshiyuki Sato,Yusuke Matsuzaki,Yuri Matsuzaki","MEGADOCK - A massively parallel software system for all-to-all protein docking analysis with pre-calculated Fourier library of protein structures","Biosupercomputing symposium (BSCS2008)",,,,,,2008,Dec.
"Yuri Matsuzaki,Yusuke Matsuzaki,Toshiyuki Sato,Yutaka Akiyama","In silico screening method of protein-protein interactions using all-to-all rigid docking and clustering: with application to pathway analysis","Biosupercomputing symposium (BSCS2008)",,,,,,2008,Dec.
"Yutaka Akiyama,Toshiyuki Sato,Yusuke Matsuzaki,Yuri Matsuzaki","Megadock - a rapid screening system for all-to-all protein docking analysis with pre-calculated fourier library of protein structures","1st Joint Workshop on Computational Science",,,,,,2008,July
"Yuri Matsuzaki,Yusuke Matsuzaki,Toshiyuki Sato,Yutaka Akiyama","Analysis of protein-protein interactions of signal transduction pathways using a docking prediction program","1st Joint Workshop on Computational Science",,,,,,2008,July
"Yusuke Matsuzaki,Yuri Matsuzaki,Toshiyuki Sato,Yutaka Akiyama","Development of post-docking system for protein-protein interaction prediction","1st Joint Workshop on Computational Science",,,,,,2008,July
"松崎 裕介,松崎 由理,佐藤 智之,秋山 泰","タンパク質間相互作用予測のためのドッキング後処理システムの開発","第13回バイオ情報学研究会","情報処理学会 研究報告",,"  2008","  58","  17-20",2008,June
"松崎 由理,松崎 裕介,佐藤 智之,秋山 泰","タンパク質ドッキング予測プログラムによるシグナル伝達系のタンパク質間相互作用解析","第13回バイオ情報学研究会","情報処理学会 研究報告",,"  2008","  58","  21-24",2008,June
"秋山 泰,松崎 裕介,佐藤 智之,藤原 康広,松崎 由理,小西 史一","形状相補性に基づくタンパク質間相互作用予測ソフトウェアと大規模並列計算機上での網羅的な予測環境の開発","第5回データ解析融合ワークショップ（公開ワークショップ）",,,,,,2008,Mar.
"松崎 由理,松崎 裕介,佐藤 智之,秋山 泰","細菌の走化性系への適用によるタンパク質間相互作用予測プログラムの評価","第5回データ解析融合ワークショップ（公開ワークショップ）",,,,,,2008,Mar.
"Yuri Matsuzaki","Modeling of signal transduction for bacterial chemotaxis using the E-Cell simulation system","Virtual Laboratory based on GRID Technology",,,,,,2008,Mar.