Development of reaction prediction system for environmental chemicals and secondary metabolites

• Project/Area Number: 18681033
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Applied genomics
• Research Institution: Kyoto University
• Principal Investigator: HATTORI Masahiro Kyoto University, 化学研究所, 助教 (60372554)
• Project Period (FY): 2006 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥12,610,000 (Direct Cost: ¥9,700,000、Indirect Cost: ¥2,910,000); Fiscal Year 2008: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000); Fiscal Year 2007: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2006: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
• Keywords: バイオインフォマティクス / ケモインフォマティクス / ケミカルゲノミクス / データベース / 代謝パスウェイ解析 / 酵素反応機構 / 反応予測 / パスウェイ解析 / ゲノム

Research Abstract

本研究では、代謝反応パスウェイのうち未解明のまま残されている部分、すなわち、薬物や環境因子などの細胞にとって通常外来物質と見られる化合物の代謝反応経路、および、植物の二次代謝産物の生合成経路などについて、代謝反応に関するケミカル情報を的確に表現する手法の開発、それら新しい知識をデータベースとして体系化する作業とデータの計算機的利用法の開発、酵素反応データに基づいた代謝経路の予測法の開発を行った。

Research Products

• [Journal Article] E-zyme : finding enzyme orthologues from the chemical transformation pattern of substrate-product pairs (2009)
  • Author(s): Yamanishi, Y., Hattori, M., Kotera, M., Goto, S., and Kanehisa, M.
  • Journal Title: Bioinformatics (in press)
  • Peer Reviewed
• [Journal Article] E-zyme : finding enzyme orthologues From the chemical transformation pattern of substrate-product pairs (2009)
  • Author(s): Yamanishi, Y., Hattori, M., Kotera, M. Goto, S., and Kanehisa, M.
  • Journal Title: Bioinformatics (in press)
  • Peer Reviewed
• [Journal Article] Generalized reaction patterns for prediction of unknown enzymatic reactions (2008)
  • Author(s): Shimizu, Y., Hattori, M., Goto, S., and Kanehisa, M.
  • Journal Title: Genome Informatics 20 Pages: 149-158
  • NAID: 130003997519
  • Peer Reviewed
• [Journal Article] Analysis of Common Substructures of Metabolic Compounds within the Different Organism Groups (2007)
  • Author(s): Muto, A., Hattori, M., and Kanehisa, M.
  • Journal Title: Genome Informatics 18 Pages: 299-307
  • NAID: 130003812152
  • Peer Reviewed
• [Journal Article] Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways (2007)
  • Author(s): Oh, M., Yamada, T., Hattori, M., Goto, S., and Kanehisa, M.
  • Journal Title: Journal of Chemical Information and Modeling 47 Pages: 1702-1712
  • Peer Reviewed
• [Journal Article] Reaction graph kernels for discovering missing enzymes in the plant secondary metabolism (2007)
  • Author(s): Saigo, H., Hattori, M., and Tsuda, K.
  • Journal Title: NIPS Workshop on Machine Learning in Computational Biology 2007
  • Peer Reviewed
• [Journal Article] Systematic analysis of enzyme-catalyzed reaction patterns and predicti on of microbial biodegradation pathways (2007)
  • Author(s): Oh, M., Yamada, T., Hattori, M., Goto, S., and Kanehisa, M.
  • Journal Title: Journal of Chemical Information and Modeling 47 Pages: 1702-1712
  • Peer Reviewed
• [Journal Article] Analysis of Common Substructures of Metabolic Compounds within the Dif ferent Organism Groups (2007)
  • Author(s): Muto, A., Hattori, M., and Kanehisa, M.
  • Journal Title: Genome Informatics 18 Pages: 299-307
  • Peer Reviewed
• [Journal Article] Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways (2007)
  • Author(s): Oh, M., Yamada, T., Hattori, M., Goto, S., Kanehisa, M.
  • Journal Title: Journal of Chemical Information and Modeling 47(in press)
• [Journal Article] Structure-activity relationships and pathway analysis of biological degradation processes (2006)
  • Author(s): Kadowaki, T., Wheelock, C.E., Hattori, M., Goto, S., Kanehisa, M.
  • Journal Title: Journal of Pesticide Science 31 (3) Pages: 273-281
  • NAID: 10018328167
• [Presentation] E-zyme : finding enzyme orthologues from the chemical transformation pattern of substrate-product pairs (2009)
  • Author(s): Yamanishi, Y., Hattori, M., Kotera, M., Goto, S., and Kanehisa, M.
  • Organizer: 17th Annual International Conference on Intelligent Systems for Molecular Biology & 8th European Conference o Computational Biology (ISMB/ECCB2009)
  • Place of Presentation: Stockholm
  • Year and Date: 2009-06-30
• [Presentation] Generalized Reaction Patterns for Prediction of Unknown Enzymatic Reactions (2009)
  • Author(s): Yugo Shimizu
  • Organizer: 8th International Workshop on Bioinformatics and Systems Biology 2008
  • Place of Presentation: Berlin, Germany
  • Year and Date: 2009-06-09
• [Presentation] 未知の酵素反応予測に向けた一般化反応パターンの開発 (2008)
  • Author(s): 清水祐吾、服部正泰、五斗進、金久實
  • Organizer: 第31回日本分子生物学会
  • Place of Presentation: 神戸
  • Year and Date: 2008-12-12
• [Presentation] 未知の酵素反応予測に向けた一般化反応パターンの開発 (2008)
  • Author(s): 清水祐吾
  • Organizer: BMB2008(第31回分子生物学会年会・第81回日本生化学会大会)
  • Place of Presentation: 神戸
  • Year and Date: 2008-12-12
• [Presentation] Generalized Reaction Patterns for Prediction of Unknown Enzymatic Reactions (2008)
  • Author(s): Shimizu, Y., Hattori, M., Goto, S., and Kanehisa, M.
  • Organizer: The 8th International Workshop on Bioinformatics and Systems Biology (IBSB2008)
  • Place of Presentation: Berlin
  • Year and Date: 2008-06-09
• [Presentation] Comprehensive Analysis of Enzymatic Reaction Mechanisms Based on the EC Classification and KEGG RPAIR Database (2007)
  • Author(s): Shimizu, Y., Hattori, M., Goto, S., and Kanehisa, M.
  • Organizer: The 2007 Annual Conference of Japanese Society for Bioinformatics (JSBi2007)
  • Place of Presentation: Tokyo
  • Year and Date: 2007-12-17
• [Presentation] Comprehensive Analysis of Enzymatic Reaction Mechanisms Based on the EC Classification and KEGG RPAIR Database (2007)
  • Author(s): Shimizu, Y., Hattori, M., Goto, S., and Kanehisa, M.
  • Organizer: The 2007 Annual Conference of Japanese Society for Bioinformatics
  • Place of Presentation: Tokyo
  • Year and Date: 2007-12-17
• [Presentation] Reaction graph kernels for discovering missing enzymes in the plant secondary metabolism (2007)
  • Author(s): Saigo, H., Hattori, M., and Tsuda, K.
  • Organizer: NIPS Workshop on Machine Learning in Computational Biology
  • Place of Presentation: Whistler, BC, Canada
  • Year and Date: 2007-12-07
• [Presentation] Analysis of Common Substructures of Metabolic Compounds within the Different Organism Groups (2007)
  • Author(s): Muto, A., Hattori, M., and Kanehisa, M.
  • Organizer: The 7th Annual International Workshop on Bioinformatics and Systems Biology (IBSB2007)
  • Place of Presentation: Tokyo
  • Year and Date: 2007-08-02
• [Presentation] Atomic transformation patterns in enzymatic reactions based on the comparison of chemical compound structures (2006)
  • Author(s): Hattori, M.
  • Organizer: Asia Hub for e-Drug Discovery Symposium 2006 (AHeDD2006)
  • Place of Presentation: Seoul, Korea
  • Year and Date: 2006-05-23
• [Book] To predict enzymatic reactions and metabolic pathways Chemoinformatics and Advanced Machine Learning Perspectives : Complex Computational Methods and Collaborative Techniques (Edited by Dr. Lodhi, H. and Dr. Yamanishi, Y.) (2009)
  • Author(s): Hattori, M., and Kotera, M.
  • Publisher: IGI Global
• [Book] Graph Kernels for Chemoinformatics, Chemoinformatics and Advanced Machine Learning Perspectives : Complex Computational Methods and Collaborative Techniques (Edited by Dr. Lodhi, H. and Dr. Yamanishi, Y.) (2009)
  • Author(s): Kashima, H., Saigo, H., Hattori, M., and Tsuda, K.
  • Publisher: IGI Global