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Prediction of protein functional sites by multivariate analysis of amino acid sequences

Research Project

Project/Area Number 63480514
Research Category

Grant-in-Aid for General Scientific Research (B)

Allocation TypeSingle-year Grants
Research Field 生物物性学
Research InstitutionKYOTO UNIVERSITY

Principal Investigator

KANEHISA Minoru  Kyoto University, Institute for Chemical Research, Professor, 化学研究所, 教授 (70183275)

Project Period (FY) 1988 – 1989
Project Status Completed (Fiscal Year 1989)
Budget Amount *help
¥6,000,000 (Direct Cost: ¥6,000,000)
Fiscal Year 1989: ¥1,000,000 (Direct Cost: ¥1,000,000)
Fiscal Year 1988: ¥5,000,000 (Direct Cost: ¥5,000,000)
KeywordsFunctional prediction of proteins / Multivariate analysis / Expert system / 判別分析 / クラスター分析 / アミノ酸指標
Research Abstract

In order to predict functional sites of proteins from their amino acid sequences, we have developed multivariate analysis and other methods and constructed databases for prediction. The starting point of our multivariate analysis method is to represent the amino acid sequence by a series of numerical values reflecting various biophysicochemical aspects of amino acid residues. For this purpose, we organized a database of amino acid indices by collecting published data for hydrophobicity and other properties. Since many of the reported indices were highly correlated, we performed a cluster analysis for grouping. Then, using discriminant analysis, we designed procedures to select important variables characterizing functional sites from a set of numerous variables defined from amino acid sequence data. The procedures were applied to the prediction of protein secondary structure segments and also to the prediction of glycosylation and phosphorylation sites. For the prediction of antigenicity determining sites, we organized a database with cross references of published peptide fragments and corresponding entries of the NBRF protein sequence database. However, our variable selection procedure did not produce satisfactory prediction. Because it was a severe limitation to represent sequence characteristics only by variables for multivariate analysis, we investigated more flexible methods. Thus, we applied an artificial intelligence method and developed an expert system. An expert system is more advantageous because it can incorporate various observations including results from multivariate analysis methods. We investigated the problem of predicting protein translocation sites in cells with this expert system approach. In summary, the multivariate analysis methods developed here are useful tools by themselves, but they can be more effective when combined with other approaches. Expert systems seem most suitable for practical applications.

Report

(3 results)
  • 1989 Annual Research Report   Final Research Report Summary
  • 1988 Annual Research Report
  • Research Products

    (21 results)

All Other

All Publications (21 results)

  • [Publications] Nakata,K.,Kanehisa,M.,and Maizel,J.V.,Jr.: "Discriminant analysis of promoter regions in E.Coil sequences." Comp.Appl.Biosci.4. 367-371 (1988)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1989 Final Research Report Summary
  • [Publications] Kanehisa,M.: "A multivariate analysis method for discriminating protein secondary structural segments." Prot.Eng.2. 87-92 (1988)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1989 Final Research Report Summary
  • [Publications] Nakai,K.,Kidera,A.,and Kanehisa,M.: "Cluster analysis of amino acid indices for prediction of protein structure and function." Prot.Eng.2. 93-100 (1988)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1989 Final Research Report Summary
  • [Publications] Naiak,K.and Kanehisa,M.: "Prediction of in-vivo modification sites of proteins from their primary structures." J.Biochem.104. 693-699 (1988)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1989 Final Research Report Summary
  • [Publications] Seto,Y.and Kanehisa,M.: "Repeat sequences of amino acids suggest the origin of protein." Bull.Inst.Chem.Res.,Kyoto Univ.66. 461-468 (1989)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1989 Final Research Report Summary
  • [Publications] Nakata, K., Kanehisa, M., and Maizel, J.V., Jr.: "Discriminant analysis of promoter regions in E. coli sequences." Comp. Appl, Biosci. 4, 367-371, 1988.

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1989 Final Research Report Summary
  • [Publications] Kanehisa, M.: "A multivariate analysis method for discriminating protein secondary structural segments." Prot. Eng. 2, 87-92, 1988.

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1989 Final Research Report Summary
  • [Publications] Nakai, K., Kidera, A., and Kanehisa, M.: "Cluster analysis of amino acid indices for prediction of protein structure and function." Prot. Eng. 2, 93-100, 1988.

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1989 Final Research Report Summary
  • [Publications] Nakai, K. and Kanehisa, M.: "Prediction of in-vivo modification sites of proteins from their primary structures." J. Biochem. 104, 693-699, 1988.

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1989 Final Research Report Summary
  • [Publications] Seto, Y. and Kanehisa, M.: "Repeat sequences of amino acids suggest the origin of protein." Bull, Inst. Chem. Res., Kyoto Univ. 66, 461-468, 1989.

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1989 Final Research Report Summary
  • [Publications] Nakata,K.,Kanehisa,M.,and Maizel,J.V.,Jr.: "Discriminant analysis of promoter regions in E.coli sequences." Comp.Appl.Biosci.4. 367-371 (1988)

    • Related Report
      1989 Annual Research Report
  • [Publications] Kanehisa,M.: "A multivariate analysis method for discriminating protein secondary structural segments." Prot.Eng.2. 87-92 (1988)

    • Related Report
      1989 Annual Research Report
  • [Publications] Nakai,K.,Kidera,A.,and Kanehisa,M.: "Cluster analysis of amino acid indices for prediction of protein structure and function." Prot.Eng.2. 93-100 (1988)

    • Related Report
      1989 Annual Research Report
  • [Publications] Nakai,K.and Kanehisa,M.: "Prediction of in-vivo modification sites of proteins from their Primary structures." J.Biochem.104. 693-699 (1988)

    • Related Report
      1989 Annual Research Report
  • [Publications] Seto,Y.and Kanehisa,M.: "Repeat sequences of amino acids suggest the origin of protein." Bull.Inst.Chem.Res.,Kyoto Univ.66. 461-468 (1989)

    • Related Report
      1989 Annual Research Report
  • [Publications] 金久寛: Protein Engineering. 2. 87-92 (1988)

    • Related Report
      1988 Annual Research Report
  • [Publications] 中井謙太: Protein Engineering. 2. 93-100 (1988)

    • Related Report
      1988 Annual Research Report
  • [Publications] 中井謙太: Journal of Biochemistry. 104. 693-699 (1988)

    • Related Report
      1988 Annual Research Report
  • [Publications] 荻原淳: 化学と工業. 41. 1094-1097 (1988)

    • Related Report
      1988 Annual Research Report
  • [Publications] 池屋森男,三木敬三郎 編: "タンパク質工学実験マニュアル" 講談社サイエンティフィック, 163-195 (1988)

    • Related Report
      1988 Annual Research Report
  • [Publications] 小野修一郎 編: "タンパク質工学" 丸善, 25-36 (1989)

    • Related Report
      1988 Annual Research Report

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Published: 1988-04-01   Modified: 2016-04-21  

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