Global extractionand analysis of protein tertiary structure patterns

• Project/Area Number: 21700323
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Bioinformatics/Life informatics
• Research Institution: Kyoto University
• Principal Investigator: HAYASHIDA Morihiro 京都大学, 化学研究所, 助教 (40402929)
• Project Period (FY): 2009 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000); Fiscal Year 2011: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2010: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2009: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
• Keywords: バイオインフォマティクス / 識別確率場 / 相互情報量 / タンパク質ドメイン / 整数計画法 / 文法圧縮 / 分割型木文法 / べき乗則 / アルゴリズム / 蛋白質 / 情報圧縮 / 類似度 / グラフ文法 / Morganインデックス

Research Abstract

We developed a graph compression method that does not depend on implementation, and proposed a similarity measure between graphs. We regarded a distance matrix between Cαatoms of a protein as an image, and proposed a grammar-based image compression method. In addition, we proposed a grammar-based tree compression method. Furthermore, we developed prediction methods using protein domains for protein-protein interactions and protein complexes

Research Products

• [Journal Article] Protein complex prediction via improved verification methods using constrained domain-domain matching (2012)
  • Author(s): Zhao, Y., Hayashida, M., Nacher, J. C., Nagamochi, H. and Akutsu, T
  • Journal Title: International Journal of Bioinformatics Research and Applications Volume: vol. 8 Issue: 3/4 Pages: 210-227
  • DOI: 10.1504/ijbra.2012.048970
  • NAID: 120005243442
  • Peer Reviewed
• [Journal Article] A quadsection algorithm for grammar-based image compression (2012)
  • Author(s): Hayashida, M., Ruan, P. and Akutsu, T.
  • Journal Title: Integrated Computer-Aided Engineering Volume: vol. 19 Issue: 1 Pages: 23-38
  • DOI: 10.3233/ica-2012-0389
  • NAID: 110007993903
  • Peer Reviewed
• [Journal Article] Measuring the similarity of protein structures using image compression algorithms (2011)
  • Author(s): Hayashida, M. and Akutsu, T
  • Journal Title: IEICE Transactions on Information and Systems Volume: vol. E94-D, no. 12 Pages: 2468-2478
  • NAID: 10030538198
  • URL: http://search.ieice.org/bin/summary.php?id=e94-d_12_2468
  • Peer Reviewed
• [Journal Article] Conditional random field approach to prediction of protein-protein interactions using domain information (2011)
  • Author(s): Hayashida, M., Kamada, M., Song, J. and Akutsu, T
  • Journal Title: BMC Systems Biology Volume: vol. 5, Suppl. 1 Issue: Suppl 1 Pages: S8-S8
  • DOI: 10.1186/1752-0509-5-s1-s8
  • NAID: 120003238942
  • Peer Reviewed
• [Journal Article] Measuring the similarity of protein structures using image compression algorithms (2011)
  • Author(s): 林田守広, 阿久津達也
  • Journal Title: IEICE Transactions on Information and Systems Volume: E94-D Pages: 2468-2478
  • NAID: 10030538198
  • Peer Reviewed
• [Journal Article] Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycan tree structures (2010)
  • Author(s): Zhao, Y., Hayashida, M.and Akutsu, T
  • Journal Title: BMC Bioinformatics Volume: vol. 11, Suppl 11 Issue: S11
  • DOI: 10.1186/1471-2105-11-s11-s4
  • NAID: 120002723148
  • Peer Reviewed
• [Journal Article] Comparing biological networks via graph compression (2010)
  • Author(s): Hayashida, M. and Akutsu, T
  • Journal Title: BMC Systems Biology Volume: vol. 4, Suppl. 2 Issue: S2
  • DOI: 10.1186/1752-0509-4-s2-s13
  • NAID: 120002561281
  • Peer Reviewed
• [Journal Article] The role of internal duplication in the evolution of multi-domain proteins (2010)
  • Author(s): Nacher, J. C., Hayashida, M.and Akutsu, T
  • Journal Title: BioSystems Volume: vol. 101, no. 2 Issue: 2 Pages: 127-135
  • DOI: 10.1016/j.biosystems.2010.05.005
  • Peer Reviewed
• [Journal Article] Comparing biological networks via graph compression (2010)
  • Author(s): 林田守広, 阿久津達也
  • Journal Title: BMC Systems Biology Volume: 4
  • NAID: 120002561281
  • Peer Reviewed
• [Journal Article] The role of internal duplication in the evolution of multi-domain proteins (2010)
  • Author(s): ナチェルホセ, 林田守広, 阿久津達也
  • Journal Title: Biosystems Volume: 101 Pages: 127-135
  • Peer Reviewed
• [Journal Article] Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycan tree structures (2010)
  • Author(s): 趙楊, 林田守広, 阿久津達也
  • Journal Title: BMC Bioinformatics Volume: 11
  • NAID: 120002723148
  • Peer Reviewed
• [Presentation] Protein complex prediction via improved verification methods using constrained domain-domain matching (2012)
  • Author(s): Zhao, Y., Hayashida, M., Nacher, J., Nagamochi, H. and Akutsu, T.
  • Organizer: The 10th Asia-Pacific Bioinformatics Conference
  • Place of Presentation: メルボルン,オーストラリア
  • Year and Date: 2012-01-19
• [Presentation] Protein complex prediction via improved verification methods using constrained domain-domain matching (2012)
  • Author(s): 趙楊, 林田守広, ナチェル ホセ, 永持仁, 阿久津達也
  • Organizer: The 10th Asia-Pacific Bioinformatics Conference
  • Place of Presentation: オーストラリア,メルボルン市
  • Year and Date: 2012-01-19
• [Presentation] Discriminative random field approach to prediction of protein residue contacts (2011)
  • Author(s): Kamada, M., Hayashida, M., Song, J. and Akutsu, T.
  • Organizer: 2011 IEEE Conference on Systems Biology
  • Place of Presentation: 珠海,中国
  • Year and Date: 2011-09-03
• [Presentation] Discriminative random field approach to prediction of protein residue contacts (2011)
  • Author(s): 鎌田真由美, 林田守広, 宋江寧, 阿久津達也
  • Organizer: 2011 IEEE Conference on Systems Biology
  • Place of Presentation: 中国,珠海市
  • Year and Date: 2011-09-03
• [Presentation] Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycan tree structures (2010)
  • Author(s): Zhao, Y., Hayashida, M.and Akutsu, T
  • Organizer: The 21st International Conference on Genome Informatics
  • Place of Presentation: 杭州,中国
  • Year and Date: 2010-12-16
• [Presentation] Conditional random field approach to prediction of protein-protein interactions using mutual information between domains (2010)
  • Author(s): Hayashida, M., Kamada, M., Song, J. and Akutsu, T
  • Organizer: The Fourth International Conference on Computational Systems Biology
  • Place of Presentation: 蘇州,中国
  • Year and Date: 2010-09-09
• [Presentation] Conditional random field approach to prediction of protein-protein interactions using mutual information between domains (2010)
  • Author(s): 林田守広, 鎌田真由美, 宋江寧, 阿久津達也
  • Organizer: The Fourth International Conference on Computational Systems Biology
  • Place of Presentation: 中国,蘇州市
  • Year and Date: 2010-09-09
• [Presentation] A quadsection algorithm for grammar-based image compression (2010)
  • Author(s): Hayashida, M., Ruan, P. and Akutsu, T.
  • Organizer: The 2010 International Conference on Advanced Science and Technology
  • Place of Presentation: 宮崎
  • Year and Date: 2010-06-25
• [Presentation] Comparing biological networks via graph compression (2009)
  • Author(s): Hayashida, M. and Akutsu, T
  • Organizer: The Third International Symposium on Optimization and Systems Biology
  • Place of Presentation: 張家界,中国
  • Year and Date: 2009-09-20
• [Presentation] Comparing biological networks via graph compression (2009)
  • Author(s): 林田守広、阿久津達也
  • Organizer: The Third International Symposium on Optimization and Systems Biology (OSB2009)
  • Place of Presentation: Zhangjiajie, China
  • Year and Date: 2009-09-20
• [Remarks]
  • URL: http://sunflower.kuicr.kyoto-u.ac.jp/morihiro/treegram/