An exhaustive all-to-all protein-protein interaction prediction algorithm based on 3-D shape complimentarity and its statistical distribution on protein surface.

• Project/Area Number: 19300102
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Bioinformatics/Life informatics
• Research Institution: Tokyo Institute of Technology
• Principal Investigator: AKIYAMA Yutaka Tokyo Institute of Technology, 大学院・情報理工学研究科, 教授 (30243091)
• Co-Investigator(Kenkyū-buntansha): 塚本 弘毅 産業技術総合研究所, 生命情報工学研究センター, 特別研究員 (90399501)
• Co-Investigator(Renkei-kenkyūsha): TSUKAMOTO Koki 産業技術総合研究所, 生命情報工学研究センター, 特別研究員 (90399501)
• Project Period (FY): 2007 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥18,460,000 (Direct Cost: ¥14,200,000、Indirect Cost: ¥4,260,000); Fiscal Year 2010: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2009: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000); Fiscal Year 2008: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000); Fiscal Year 2007: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
• Keywords: コンピュータシミュレーション / 蛋白質 / ドッキング / 高性能計算 / バイオインフォマティクス

Research Abstract

We have developed a novel computing method for rigid-body protein docking and applied it to Protein-Protein Interaction network prediction in systems biology. The original rPSC model uses only real numbers while ZDOCK's PSC uses complex numbers and then our method is four-times faster than ZDOCK without loss of sensitivity. We also proposed a method to dynamically change balance between shape complementarity and electrostatics. Total prediction accuracy is improved with clustering and reranking as post-processing.

Research Products

• [Journal Article] Docking-calculation-based Method for Predicting Protein-RNA Interactions (2011)
  • Author(s): Masahito Ohue, Yuri Matsuzaki, Yutaka Akiyama
  • Journal Title: Genome Informatics Volume: 25
  • NAID: 130004567841
  • Peer Reviewed
• [Journal Article] 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 (2010)
  • Author(s): 大上雅史, 松崎由理, 松崎祐介, 佐藤智之, 秋山泰, MEGADOCK
  • Journal Title: 情報処理学会論文誌(TOM) 3(3) Pages: 91-106
  • Peer Reviewed
• [Journal Article] In silico classification of major clearance pathways of drugs with their physicochemical parameters (2010)
  • Author(s): Makiko Kusama, Kouta Toshimoto, Kazuya Maeda, Yuka Hirai, Satoki Imai, Koji Chiba, Yutaka Akiyama, Yuichi Sugiyama
  • Journal Title: Drug Metabolism and Disposition 28(8) Pages: 1362-1370
  • Peer Reviewed
• [Journal Article] Computer prediction of protein-protein interaction network using MEGADOCK-application to systems biology (2010)
  • Author(s): Yuri Matsuzaki, Masahito Ohue, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama
  • Journal Title: TSUBAME e-Science Journal 2 Pages: 34-37
• [Journal Article] Exhaustive protein-protein interaction network prediction by using MEGADOCK (2010)
  • Author(s): Yutaka Akiyama, Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue
  • Journal Title: BioSupercomputing Newsletter 3 Pages: 8-8
• [Journal Article] 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 (2010)
  • Author(s): 大上雅史, 松崎由理, 松崎裕介, 佐藤智之, 秋山泰
  • Journal Title: 情報処理学会論文誌 数理モデル化と応用(TOM) Volume: 3(3) Pages: 91-106
  • NAID: 110007993887
  • Peer Reviewed
• [Journal Article] Analysis of protein-protein docking decoys using interaction fingerprints : application to the reconstruction of CaM-ligand complexes (2010)
  • Author(s): Nobuyuki Uchikoga, Takatsugu Hirokawa
  • Journal Title: BMC Bioinformatics Volume: 11(236) Pages: 1-10
  • Peer Reviewed
• [Journal Article] In silico classification of major clearance pathways of drugs with their physiochemical parameters. (2010)
  • Author(s): Makiko Kusama, Kouta Toshimoto, Kazuya Maeda, Yuka Hirai, Satoki Imai, Koji Chiba, Yutaka Akiyama, Yuichi Sugiyama
  • Journal Title: Drug Metabolism and Disposition Volume: 28(8) Pages: 1362-1370
  • Peer Reviewed
• [Journal Article] Exhaustive protein-protein interaction network prediction by using MEGADOCK (2010)
  • Author(s): Yutaka Akiyama, Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue
  • Journal Title: BioSupercomputing Newsletter Volume: 3 Pages: 8-8
• [Journal Article] Computer prediction of protein-protein interaction network using MEGADOCK -- application to systems biology. (2010)
  • Author(s): Yuri Matsuzaki, Masahito Ohue, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama
  • Journal Title: TSUBAME e-Science Journal Volume: 2 Pages: 34-37
• [Journal Article] In silico screening of protein-protein interactions with all-to-all rigid docking and clustering : an application to pathway analysis (2009)
  • Author(s): 松崎由理, 松崎祐介, 佐藤智之, 秋山泰
  • Journal Title: Journal of Bioinformatics and Computational Biology 7(6) Pages: 991-1012
  • Peer Reviewed
• [Journal Article] In silico screening of protein-protein interactions with all-to-all rigid docking and clustering: an application to pathway analysis (2009)
  • Author(s): Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
  • Journal Title: Journal of Bioinformatics and Computational Biology 7(6) Pages: 991-1012
  • Peer Reviewed
• [Journal Article] In silico screening of protein-protein interactions with all-to-all rigid doc king and clustering : an application to pathway analysis (2009)
  • Author(s): Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
  • Journal Title: Journal of Bioinformatics and Computational Biology 7(6) Pages: 991-1012
  • Peer Reviewed
• [Journal Article] Development of an affinity evaluation and prediction system by using the shape complementarity characteristic between proteins (2008)
  • Author(s): Koki Tsukamoto, Tatsuya Yoshikawa, Yuichiro Hourai, Kazuhiko Fukui, Yutaka Akiyama
  • Journal Title: Journal of Bioinformatics and Computational Biology 6(6) Pages: 1133-1156
  • Peer Reviewed
• [Journal Article] evaluation and prediction system by using the shape complementarity characteristic between proteins (2008)
  • Author(s): Koki Tsukamoto, Tatsuya Yoshikawa, Yuichiro Hourai, Kazuhiko Fukui, Yutaka Akiyama, Development of an affinity
  • Journal Title: Journal of Bioinformatics and Computational Biology 6(6) Pages: 1133-1156
  • Peer Reviewed
• [Journal Article] Development of an affinity evaluation and prediction system by using the shape complementarity characteristic between proteins (2008)
  • Author(s): Koki Tsukamoto, Tatsuya Yoshikawa, Yuichiro Hourai, Kazuhiko Fukui, Yutaka Akiyama
  • Journal Title: Journal of Bioinformatics and Computational Biology 6 (6) Pages: 1133-1156
  • Peer Reviewed
• [Journal Article] Optimization and Evaluation of Parallel Molecular Dynamics Simulation on Blue Gene/L (2007)
  • Author(s): M. Sekijima J. Doi, T. Noguchi, Y. Akiyama, S. Shimizu
  • Journal Title: Proceedings of the IASTED International Conference on Parallel and Distributed Computer and Networks (PDCN2007) 1 Pages: 257-262
  • Peer Reviewed
• [Journal Article] Systematic Comparison of Catalytic Mechanisms of Hydrolysis and Transfer Reactions Classified in the EzCatDB Database (2007)
  • Author(s): Nagano, N., Noguchi, T., Akiyama, Y.
  • Journal Title: PROTEINS: Structure, Function, and Bioin formatics 66(1) Pages: 147-159
  • Peer Reviewed
• [Journal Article] Docking-calculation-based Method for Predicting Protein-RNA Interactions, Genome
  • Author(s): 大上雅史, 松崎由理, 秋山泰
  • Journal Title: Informatics in press Pages: 25-25
  • Peer Reviewed
• [Presentation] タンパク質ドッキング計算結果の可視化とその解析 (2011)
  • Author(s): 山本航平, 大上雅史, 松崎由理, 石田貴士, 秋山泰
  • Organizer: 第73回情報処理学会全国大会
  • Place of Presentation: 東京工業大学(東京)
  • Year and Date: 2011-03-02
• [Presentation] タンパク質-リガンド間の結合性解析の自動パイプライン化 (2011)
  • Author(s): 尾渡裕成, 関嶋政和, 秋山泰
  • Organizer: 第73回情報処理学会全国大会
  • Place of Presentation: 東京工業大学(東京)
  • Year and Date: 2011-03-02
• [Presentation] 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 (2011)
  • Author(s): 大上雅史, 松崎由理, 秋山泰
  • Organizer: 第73回情報処理学会全国大会
  • Place of Presentation: 東京工業大学(東京)
  • Year and Date: 2011-03-02
• [Presentation] 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 (2011)
  • Author(s): 松崎由理, 内古閑伸之, 大上雅史, 石田貴士, 秋山泰
  • Organizer: 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
  • Place of Presentation: 甲南大学(神戸)
  • Year and Date: 2011-02-21
• [Presentation] 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問題における前処理の評価 (2011)
  • Author(s): 内古閑伸之, 広川貴次, 秋山泰
  • Organizer: 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
  • Place of Presentation: 甲南大学(神戸)
  • Year and Date: 2011-02-21
• [Presentation] タンパク質とRNAの立体構造に基づいた網羅的計算による相互作用予測 (2011)
  • Author(s): 大上雅史, 松崎由理, 内古閑伸之, 石田貴士, 秋山泰
  • Organizer: 2011年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(HPCS2011)
  • Place of Presentation: 産業技術総合研究所(筑波)
  • Year and Date: 2011-01-19
• [Presentation] Exhaustive Protein-Protein Interaction Network Prediction by MEGADOCK (2010)
  • Author(s): 秋山泰
  • Organizer: Asia Hub for e-Drug Discovery Symposium AHeDD 2010
  • Place of Presentation: Yonsei University(韓国)(招待講演)
  • Year and Date: 2010-12-18
• [Presentation] Exhaustive Protein-Protein Interaction Network Prediction by MEGADOCK (2010)
  • Author(s): Yutaka Akiyama
  • Organizer: Asia Hub for eDrug Discovery (AHeDD) Symoposium 2010
  • Place of Presentation: Yonsei University (韓国) 招待講演
  • Year and Date: 2010-12-18
• [Presentation] Post-docking analysis with interaction fingerprint (2010)
  • Author(s): Nobuyuki Uchikoga, Takatsugu Hirokawa, Yutaka Akiyama
  • Organizer: Asia Hub for eDrug Discovery (AHeDD) Symoposium 2010
  • Place of Presentation: Yonsei University (韓国)
  • Year and Date: 2010-12-18
• [Presentation] Exhaustive protein-protein interaction prediction with MEGADOCK and its application to signaling pathway estimation (2010)
  • Author(s): Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Takashi Ishida, Yutaka Akiyama
  • Organizer: Asia Hub for eDrug Discovery (AHeDD) Symoposium 2010
  • Place of Presentation: Yonsei University (韓国)
  • Year and Date: 2010-12-18
• [Presentation] Binding Analysis of Neuraminidase Inhibitors by Fragment Molecular Orbital Calculation (2010)
  • Author(s): Yusei Owatari, Masakazu Sekijima, Yutaka Akiyama
  • Organizer: Asia Hub for eDrug Discovery (AHeDD) Symoposium 2010
  • Place of Presentation: Yonsei University (韓国)
  • Year and Date: 2010-12-18
• [Presentation] 相互作用プロファイルによるタンパク質複合体予測のポストドッキング解析 (2010)
  • Author(s): 内古閑伸之, 広川貴次, 秋山泰
  • Organizer: 第38回構造活性相関シンポジウム
  • Place of Presentation: 徳島大学(徳島)
  • Year and Date: 2010-10-30
• [Presentation] A computational screening system of protein-protein interactions : connecting protein structural information to biological pathway estimation (2010)
  • Author(s): 松崎由理, 大上雅史, 松崎裕介, 佐藤智之, 秋山泰
  • Organizer: 11th International Conference on Systems Biology (ICSB 2010)
  • Place of Presentation: Edinburgh Int'l Conference Centre(英国)
  • Year and Date: 2010-10-12
• [Presentation] A computational screening system of protein-protein interactions : connecting protein structural information to biological pathway estimation (2010)
  • Author(s): Yuri Matsuzaki, Masahito Ohue, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
  • Organizer: 11th International Conference on Systems Biology (ICSB 2010)
  • Place of Presentation: Edinburgh International Conference Centre (英国)
  • Year and Date: 2010-10-12
• [Presentation] 立体構造情報を用いた網羅的計算によるタンパク質間相互作用ネットワーク予測 (2010)
  • Author(s): 大上雅史, 松崎由理, 秋山泰
  • Organizer: 生命情報科学若手の会 第2回研究会
  • Place of Presentation: 遺伝学研究所(三島)
  • Year and Date: 2010-10-09
• [Presentation] In silico prediction of PPI network with structure-based all-to-all docking (2010)
  • Author(s): 大上雅史, 松崎由理, 松崎裕介, 佐藤智之, 秋山泰
  • Organizer: InCoB2010-the 9th International Conference on Bioinformatics
  • Place of Presentation: Waseda University(東京)
  • Year and Date: 2010-09-26
• [Presentation] In silico prediction of PPI network with structure-based all-to-all docking (2010)
  • Author(s): Masahito Ohue, Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
  • Organizer: InCoB2010 - the 9th International Conference on Bioinformatics
  • Place of Presentation: 早稲田大学(東京)
  • Year and Date: 2010-09-26
• [Presentation] Searching near-native decoys from various types of protein complexes by cluster analysis with Interaction Finger Print (2010)
  • Author(s): Nobuyuki Uchikoga, Takatsugu Hirokawa, Yutaka Akiyama
  • Organizer: The 48th Annual Meeting of the Biophysical Soc.of Japan
  • Place of Presentation: Tohoku University(仙台)
  • Year and Date: 2010-09-22
• [Presentation] Searching near-native decoys from various types of protein complexes by cluster analysis with Interaction Finger Print (2010)
  • Author(s): Nobuyuki Uchikoga, Takatsugu Hirokawa, Yutaka Akiyama
  • Organizer: The 48th Annual Meeting of the Biophysical Society of Japan
  • Place of Presentation: 東北大学(仙台)
  • Year and Date: 2010-09-22
• [Presentation] Cluster analysis in post-docking process for rigid- body docking problem by using Interaction Fingerprints (2010)
  • Author(s): Nobuyuki Uchikoga, Takatsugu Hirokawa, Yutaka Akiyama
  • Organizer: CBRC2010
  • Place of Presentation: Computational Biology Res.Center(東京)
  • Year and Date: 2010-07-28
• [Presentation] Cluster analysis in post-docking process for rigid-body docking problem by using Interaction Fingerprints (2010)
  • Author(s): Nobuyuki Uchikoga, Takatsugu Hirokawa, Yutaka Akiyama
  • Organizer: Computational Biology Research Center Workshop 2010 (CBRC2010)
  • Place of Presentation: 産業技術総合研究所(東京)
  • Year and Date: 2010-07-28
• [Presentation] 単純ベイズ確率モデルの導入による天然変性蛋白質領域予測の改良 (2010)
  • Author(s): 石田貴士, 秋山泰
  • Organizer: 情報処理学会 第21回 バイオ情報学研究発表会
  • Place of Presentation: 琉球大学(那覇)
  • Year and Date: 2010-06-19
• [Presentation] 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 (2010)
  • Author(s): 大上雅史, 松崎由理, 松崎裕介, 佐藤智之, 秋山泰
  • Organizer: 情報処理学会 第78回 数理モデル化と問題解決研究発表会
  • Place of Presentation: 群馬大学(高崎)
  • Year and Date: 2010-05-21
• [Presentation] A computational screening system of protein-protein interactions : connecting protein structural information to biological pathway estimation (2010)
  • Author(s): 松崎由理, 大上雅史, 松崎裕介, 佐藤智之, 秋山泰
  • Organizer: Computing with GPUs, Cells, and Multicores
  • Place of Presentation: ETH Zurich(スイス)
  • Year and Date: 2010-05-10
• [Presentation] A computational screening system of protein-protein interactions : connecting protein structural information to biological pathway estimation (2010)
  • Author(s): Yuri Matsuzaki, Masahito Ohue, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
  • Organizer: ETHZ - Tokyo Tech Workshop : Computing with GPUs, Cells, and Multicores
  • Place of Presentation: ETH Zurich (スイス)
  • Year and Date: 2010-05-10
• [Presentation] A computatioal screening system of protein-ptotein interactions : connecting structural information to pathway estimation (2010)
  • Author(s): Yuri Matsuzaki, Yusuke Matsuzaki, Masahito Ohue, Toshiyuki Sato, Yutaka Akiyama
  • Organizer: The 2nd Biosupercomputing Symposium (BSCS)
  • Place of Presentation: MY PLAZA ホール(東京)
  • Year and Date: 2010-03-18
• [Presentation] MEGADOCK : An all-to all protein-protein interaction prediction system-Improving the sccuracy using boosting and binding energy reranking (2010)
  • Author(s): Masahito Ohue, Yusuke Matsuzaki, Yuri Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
  • Organizer: The 2nd Biosupercomputing Symposium (BSCS)
  • Place of Presentation: MY PLAZA ホール(東京)
  • Year and Date: 2010-03-18
• [Presentation] 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 (2010)
  • Author(s): 松崎裕介, 大上雅史, 松崎由理, 佐藤智之, 関嶋政和, 秋山泰
  • Organizer: 情報処理学会第20回バイオ情報学研究会
  • Place of Presentation: 北陸先端大学(金沢)
  • Year and Date: 2010-03-04
• [Presentation] 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 (2010)
  • Author(s): 大上雅史, 松崎裕介, 松崎由理, 佐藤智之, 秋山泰
  • Organizer: 情報処理学会 第20回バイオ情報学研究会
  • Place of Presentation: 北陸先端大学(金沢)
  • Year and Date: 2010-03-04
• [Presentation] 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 (2010)
  • Author(s): 松崎裕介, 大上雅史, 松崎由理, 佐藤智之, 関嶋政和, 秋山泰
  • Organizer: 情報処理学会 第20回バイオ情報学研究会
  • Place of Presentation: 北陸先端大学(金沢)
  • Year and Date: 2010-03-04
• [Presentation] 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 (2010)
  • Author(s): 大上雅史, 松崎裕介, 松崎由理, 佐藤智之, 秋山泰
  • Organizer: 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)
  • Place of Presentation: 淡路夢舞台国際会議場(淡路)
  • Year and Date: 2010-03-01
• [Presentation] 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 (2010)
  • Author(s): 大上雅史, 松崎裕介, 松崎由理, 佐藤智之, 秋山泰
  • Organizer: 情報処理学会バイオ情報学研究会SIGBIO-20-3
• [Presentation] 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 (2010)
  • Author(s): 松崎裕介, 大上雅史, 松崎由理, 佐藤智之, 関嶋政和, 秋山泰
  • Organizer: 情処SIGBIO-20-4
• [Presentation] Improvement of all-to-all protein-protein interaction prediction system MEGADOCK (2009)
  • Author(s): 大上雅史, 松崎裕介, 松崎由理, 秋山泰
  • Organizer: Genome Informatics Workshop (GIW2009)
  • Place of Presentation: Pacifico Yokohama(横浜)
  • Year and Date: 2009-12-14
• [Presentation] Improvement of all-to-all protein-protein interaction prediction system MEGADOCK (2009)
  • Author(s): Masahito Ohue, Yusuke Matsuzaki, Yuri Matsuzaki, Yutaka Akiyama
  • Organizer: The 20th International Conference on Genome Informatics Workshop (GIW2009)
  • Place of Presentation: パシフィコ横浜(横浜)
  • Year and Date: 2009-12-14
• [Presentation] A computational screening system of protein-protein interactions using tertiary structure data : an application to signaling pathway analysis (2009)
  • Author(s): Yuri Matsuzaki, Yusuke Matsuzaki, Masahito Ohue, Toshiyuki Sato, Yutaka Akiyama
  • Organizer: BIOINFO 2009 CBI-KSBSB Joint Conference
  • Place of Presentation: Haeundae Grand Hotel(韓国)
  • Year and Date: 2009-11-04
• [Presentation] Protein structure sampling based on molecular dynamics and improvement of docking prediction (2009)
  • Author(s): Yusuke Matsuzaki, Yuri Matsuzaki, Masakazu Sekijima, Yutaka Akiyama
  • Organizer: BIOINFO 2009 CBI-KSBSB Joint Conference
  • Place of Presentation: Haeundae Grand Hotel(韓国)
  • Year and Date: 2009-11-04
• [Presentation] Binding analysis of neuraminidase inhibitors by fragment MO calculation (2009)
  • Author(s): Yusei Owatari, Masakazu Sekijima, Yutaka Akiyama
  • Organizer: BIOINFO 2009 CBI-KSBSB Joint Conference
  • Place of Presentation: Haeundae Grand Hotel(韓国)
  • Year and Date: 2009-11-04
• [Presentation] Improvement of all-to-all protein-protein interaction prediction system MEGADOCK (2009)
  • Author(s): Masahito Ohue, Yusuke Matsuzaki, Yuri Matsuzaki, Yutaka Akiyama
  • Organizer: BIOINFO 2009 CBI-KSBSB Joint Conference
  • Place of Presentation: Haeundae Grand Hotel(韓国)
  • Year and Date: 2009-11-04
• [Presentation] 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 (2009)
  • Author(s): 大上雅史, 松崎裕介, 松崎由理, 秋山泰
  • Organizer: 情報処理学会 第18回バイオ情報学会研究会
  • Place of Presentation: 北海道大学(札幌)
  • Year and Date: 2009-09-17
• [Presentation] 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 (2009)
  • Author(s): 松崎裕介, 松崎由理, 関嶋政和, 秋山泰
  • Organizer: 情報処理学会 第18回バイオ情報学会研究会
  • Place of Presentation: 北海道大学(札幌)
  • Year and Date: 2009-09-17
• [Presentation] フラグメントMO法によるノイラミニダーゼ阻害薬の結合性解析 (2009)
  • Author(s): 尾渡裕成, 関嶋政和, 秋山泰
  • Organizer: 情報処理学会 第18回バイオ情報学会研究会
  • Place of Presentation: 北海道大学(札幌)
  • Year and Date: 2009-09-17
• [Presentation] In silico screening of proteinprotein interactions with all-to-all rigid docking and clustering : an application to pathway analysis (2009)
  • Author(s): 松崎由理, 松崎裕介, 大上雅史, 佐藤智之, 秋山泰
  • Organizer: The 10th International Conference on Systems Biology (ICSB 2009)
  • Place of Presentation: Stanford University(米国)
  • Year and Date: 2009-09-01
• [Presentation] In silico screening of protein-protein interactions with all-to-all rigid doc king and clustering : an application to pathway analysis (2009)
  • Author(s): Yuri Matsuzaki, Yusuke Matsuzaki, Masahito Ohue, Toshiyuki Sato, Yutaka Akiyama
  • Organizer: The 10th International Conference on Systems Biology (ICSB 2009)
  • Place of Presentation: Stanford大学(米国)
  • Year and Date: 2009-09-01
• [Presentation] A computational screening system of protein-protein interactions using tertiary structure data : with applicatio to pathway analysis (2009)
  • Author(s): Yuri Matsuzaki, Yusuke Matsuzaki, Masahito Ohue, Toshiyuki Sato, Yutaka Akiyama
  • Organizer: Joint Computational Science Workshop 2009
  • Place of Presentation: 理研横浜研究所(鶴見)
  • Year and Date: 2009-07-09
• [Presentation] 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 (2009)
  • Author(s): 大上雅史, 松崎裕介, 松崎由理, 佐藤智之, 秋山泰
  • Organizer: 情報処理学会 第17回バイオ情報学会研究会
  • Place of Presentation: 沖縄科学技術研究基盤整備機構(沖縄)
  • Year and Date: 2009-05-26
• [Presentation] 物理化学的相互作用の導入によるタンパク質間相互作用予測システムの高精度化 (2009)
  • Author(s): 大上雅史, 秋山泰
  • Organizer: 第8回データ解析融合ワークショップ
  • Place of Presentation: 学術総合センター(東京)
  • Year and Date: 2009-03-16
• [Presentation] 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 (2009)
  • Author(s): 松崎 由理, 松崎 裕介, 大上 雅史, 佐藤 智之, 秋山 泰
  • Organizer: 第8回データ解析融合ワークショップ
  • Place of Presentation: 学術総合センター(東京)
  • Year and Date: 2009-03-16
• [Presentation] 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 (2009)
  • Author(s): 大上雅史, 松崎裕介, 松崎由理, 佐藤智之, 秋山泰
  • Organizer: 情処SIGBIO-17-4
• [Presentation] MEGADOCK - A massively parallel software system for all-to-all protein docking analysis with pre-calculated Fourier library of protein structures (2008)
  • Author(s): Yutaka Akiyama, Toshiyuki Sato, Yusuke Matsuzaki, Yuri Matsuzaki
  • Organizer: バイオスーパーコンピューティング・シンポジウム(BSCS)2008
  • Place of Presentation: 丸の内マイプラザ(東京)
  • Year and Date: 2008-12-25
• [Presentation] In Silico Screening Method of Protein-protein Interactions Using All-to-all Rigid Docking and Clustering : with Application to Pathway Analysis (2008)
  • Author(s): Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
  • Organizer: バイオスーパーコンピューティング・シンポジウム(BSCS)2008
  • Place of Presentation: 丸の内マイプラザ(東京)
  • Year and Date: 2008-12-25
• [Presentation] Megadock-a rapid screening system for all-to-all protein docking analysis with precalculated fourier library of protein structures (2008)
  • Author(s): 秋山泰, 佐藤智之, 松崎裕介, 松崎由理
  • Organizer: The 2008 Annual Conference of the Japanese Society for Bioinformatics(JSBi2008)
  • Place of Presentation: 千里ライフサイエンスセンター(大阪
  • Year and Date: 2008-12-15
• [Presentation] Megadock - a rapid screening system for all-to-all protein docking analysis with precalculated fourier library of protein structures (2008)
  • Author(s): Yutaka Akiyama, Toshiyuki Sato, Yusuke Matsuzaki, Yuri Matsuzaki
  • Organizer: The 2008 Annual Conference of the Japanese Society for Bioinformatics (JSBi2008)
  • Place of Presentation: 千里ライフサイエンスセンター(大阪)
  • Year and Date: 2008-12-15
• [Presentation] Virtual screening of protein-protein interactions : an application to known signal transduction systems (2008)
  • Author(s): Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
  • Organizer: The 2008 Annual Conference of the Japanese Society for Bioinformatics (JSBi2008)
  • Place of Presentation: 千里ライフサイエンスセンター(大阪)
  • Year and Date: 2008-12-15
• [Presentation] Predicting protein-protein interactions with a peta-flops computer : Techniques and potential applications to systems biology research (2008)
  • Author(s): Yutaka Akiyama, Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Satoshi Matsuoka
  • Organizer: The ninth international conference of KSBSB (Bioinfo2008)
  • Place of Presentation: 忠北大学校(韓国)
  • Year and Date: 2008-11-13
• [Presentation] Megadock - a rapid screening system for all-to-all protein docking analysis with pre-calculated fourier library of protein structures (2008)
  • Author(s): Yutaka Akiyama, Toshiyuki Sato, Yusuke Matsuzaki, Yuri Matsuzaki
  • Organizer: 1st Joint Workshop on Computational Science
  • Place of Presentation: 理化学研究所(和光)
  • Year and Date: 2008-07-07
• [Presentation] Development of post・docking system for protein-protein interaction prediction (2008)
  • Author(s): Yusuke Matsuzaki, Yuri Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
  • Organizer: 1st Joint Workshop on Computational Science
  • Place of Presentation: 理化学研究所(和光)
  • Year and Date: 2008-07-07
• [Presentation] Analysis of protein・protein interactions of signal transduction pathways using a docking prediction program (2008)
  • Author(s): Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama
  • Organizer: 1st Joint Workshop on Computational Science
  • Place of Presentation: 理化学研究所(和光)
  • Year and Date: 2008-07-07
• [Presentation] 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 (2008)
  • Author(s): 松崎 裕介, 松崎 由理, 佐藤 智之, 秋山 泰
  • Organizer: 情報処理学会 第13回バイオ情報学研究会
  • Place of Presentation: 琉球大学(沖縄)
  • Year and Date: 2008-06-26
• [Presentation] 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 (2008)
  • Author(s): 松崎 由理, 松崎 裕介, 佐藤 智之, 秋山 泰
  • Organizer: 情報処理学会 第13回バイオ情報学研究会
  • Place of Presentation: 琉球大学(沖縄)
  • Year and Date: 2008-06-26
• [Remarks] ホームページ
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• [Remarks]
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