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Development of novel algorithm to detect enzyme active-sites considering cofactors

Research Project

Project/Area Number 23500373
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionNational Institute of Advanced Industrial Science and Technology

Principal Investigator

NAGANO Nozomi  独立行政法人産業技術総合研究所, 生命情報工学研究センター, 主任研究員 (70357648)

Co-Investigator(Kenkyū-buntansha) KATO Tsuyoshi  群馬大学, 工学研究科, 准教授 (40401236)
Project Period (FY) 2011 – 2013
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2013: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2012: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2011: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Keywords酵素 / 活性部位 / 予測法 / 重みつき偏差 / カーネル / 補酵素 / 構造 / 酵素反応
Research Abstract

Prediction of active sites in enzyme proteins is extremely essential not only for protein sciences but also for practical applications. Because enzyme reaction mechanisms are based on the local structures of enzyme active sites, a simple measurement, mean square deviation, has been used to compare such local structures in proteins so far. In order to improve the ability of such a simple measurement, various kinds of template-based methods that compare the local sites have been developed to date. In this work, parameters for the deviation was introduced. Moreover, the Bregman Divergence Regularized Machine was also employed to develop a new machine learning algorithm that determines the parameters of the square deviation. Experimental results showed that the proposed methods possess promising search performance.

Report

(4 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Research-status Report
  • 2011 Research-status Report
  • Research Products

    (29 results)

All 2014 2013 2012 Other

All Journal Article (10 results) (of which Peer Reviewed: 6 results) Presentation (14 results) Remarks (5 results)

  • [Journal Article] 平均多項式カーネルと動画像認識およびブレインマシンインタフェースへの応用2014

    • Author(s)
      レラトーレイサ, 廣橋義寛, 伊藤栄祐, 加藤毅
    • Journal Title

      電子情報通信学会技術報告書

      Volume: 113巻 Pages: 281-286

    • Related Report
      2013 Final Research Report
  • [Journal Article] Mean Polynomial Kernel and Its Application to Vector Sequence Recognition2014

    • Author(s)
      Raissa Relator, Yoshihiro Hirohashi, Eisuke Ito, Tsuyoshi Kato
    • Journal Title

      IEICE Transactions on Information and Systems

      Volume: vol.E97-D(in press)

    • NAID

      130004519281

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] 多項式カーネルと動画像認識およびブレインマシンインタフェースへの応用2014

    • Author(s)
      レラトーレイサ、廣橋義寛、伊藤栄祐、加藤毅
    • Journal Title

      電子情報通信学会技術報告書

      Volume: 113 Pages: 281-286

    • Related Report
      2013 Annual Research Report
  • [Journal Article] Mean Polynomial Kernel and Its Application to Vector Sequence Recognition2014

    • Author(s)
      Raissa Relator, Yoshihiro Hirohashi, Eisuke Ito, Tsuyoshi Kato
    • Journal Title

      IEICE Transactions on Information & Systems

      Volume: E97-D

    • NAID

      130004519281

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Bregman Divergence Regularized Machine による酵素活性部位予測2013

    • Author(s)
      レラトーレイサ, 加藤毅, 長野希美
    • Journal Title

      電子情報通信学会技術報告書

      Volume: 113巻 Pages: 61-66

    • Related Report
      2013 Final Research Report
  • [Journal Article] A Discriminative Metric Learning Algorithm for Face Recognition2013

    • Author(s)
      Tsuyoshi Kato, Wataru Takei, Shinichiro Omachi
    • Journal Title

      IPSJ Transactions on Computer Vision and Applications

      Volume: vol.5 Pages: 85-89

    • NAID

      130003384038

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Richard Lemence, Improved protein-ligand prediction using kernel weighted canonical correlation analysis2013

    • Author(s)
      Raissa Relator, Tsuyoshi Kato
    • Journal Title

      IPSJ Transactions on Bioinformatics

      Volume: vol.6 Pages: 18-28

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Bregman Divergence Regularized Machine による酵素活性部位予測2013

    • Author(s)
      レラトーレイサ、加藤毅、長野希美
    • Journal Title

      電子情報通信学会技術報告書

      Volume: 113 Pages: 61-66

    • Related Report
      2013 Annual Research Report
  • [Journal Article] A Discriminative Metric Learning Algorithm for Face Recognition2013

    • Author(s)
      Tsuyoshi Kato, Wataru Takei, Shinichiro Omachi
    • Journal Title

      IPSJ Transactions on Computer Vision and Applications

      Volume: 5 Issue: 0 Pages: 85-89

    • DOI

      10.2197/ipsjtcva.5.85

    • NAID

      130003369484

    • ISSN
      1882-6695
    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Improved Protein-ligand Prediction Using Kernel Weighted Canonical Correlation Analysis2013

    • Author(s)
      Raissa Relator, Tsuyoshi Kato, Richard Lemence
    • Journal Title

      IPSJ Transactions on Bioinformatics

      Volume: 6 Issue: 0 Pages: 18-28

    • DOI

      10.2197/ipsjtbio.6.18

    • NAID

      130003369494

    • ISSN
      1882-6679
    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Presentation] 平均多項式カーネルと動画像認識およびブレインマシンインタフェースへの応用2014

    • Author(s)
      レラトーレイサ, 廣橋義寛, 伊藤栄祐, 加藤毅
    • Organizer
      PRMU2014
    • Place of Presentation
      大阪大学(大阪)
    • Related Report
      2013 Final Research Report
  • [Presentation] 平均多項式カーネルと動画像認識およびブレインマシンインタフェースへの応用2014

    • Author(s)
      レラトーレイサ、廣橋義寛、伊藤栄祐、加藤毅
    • Organizer
      PRMU2014
    • Place of Presentation
      大阪大学(大阪府)
    • Related Report
      2013 Annual Research Report
  • [Presentation] A random-forest based method that can predict detailed enzyme functions and also identify specificity determining residues2013

    • Author(s)
      長尾知生子, 長野希美, 水口賢司
    • Organizer
      CBI学会2013年大会-生命医薬情報学連合会-
    • Place of Presentation
      タワーホール船堀(東京)
    • Year and Date
      2013-10-29
    • Related Report
      2013 Final Research Report
  • [Presentation] A Discriminative Metric Learning Algorithm for Face Recognition2013

    • Author(s)
      Tsuyoshi Kato, Wataru Takei, Shinichiro Omachi
    • Organizer
      MIRU2013
    • Place of Presentation
      国立情報学研究所(東京)
    • Related Report
      2013 Final Research Report
  • [Presentation] Bregman Divergence Regularized Machine による酵素活性部位予測2013

    • Author(s)
      レラトーレイサ, 加藤毅, 長野希美
    • Organizer
      PRMU2013
    • Place of Presentation
      三重大学(三重)
    • Related Report
      2013 Final Research Report
  • [Presentation] Bregman Divergence Regularized Machine による酵素活性部位予測2013

    • Author(s)
      レラトーレイサ、加藤毅、長野希美
    • Organizer
      PRMU2013
    • Place of Presentation
      三重大学(三重県)
    • Related Report
      2013 Annual Research Report
  • [Presentation] A Discriminative Metric Learning Algorithm for Face Recognition.2013

    • Author(s)
      Tsuyoshi Kato, Wataru Takei, Shinichiro Omachi
    • Organizer
      MIRU2013
    • Place of Presentation
      国立情報学研究所(東京都)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Analysis of enzyme structures and functions/酵素の構造・機能の解析2012

    • Author(s)
      長野希美
    • Organizer
      BiWO2012
    • Place of Presentation
      産総研臨海副都心センター(東京)
    • Year and Date
      2012-10-31
    • Related Report
      2013 Final Research Report
  • [Presentation] Enzyme function prediction using active sites and ligand binding sites information2012

    • Author(s)
      Chioko Nagao, Nozomi Nagano, Kenji Mizuguchi
    • Organizer
      第12回日本蛋白質科学会年会
    • Place of Presentation
      名古屋国際会議場(愛知)
    • Year and Date
      2012-06-21
    • Related Report
      2013 Final Research Report
  • [Presentation] Metric-learning based active site prediction for enzyme proteins2012

    • Author(s)
      加 藤毅, 長野希美
    • Organizer
      BiWO2011
    • Place of Presentation
      産総研臨海副都心センター(東京)
    • Year and Date
      2012-01-26
    • Related Report
      2013 Final Research Report
  • [Presentation] Metric-learning based active site prediction for enzyme proteins2012

    • Author(s)
      加藤毅、長野希美
    • Organizer
      BiWO2011
    • Place of Presentation
      産総研臨海副都心センター(東京都)
    • Related Report
      2011 Research-status Report
  • [Presentation] A random-forest based method that can predict detailed enzyme functions and also identify specificity determining residues

    • Author(s)
      長尾知生子、長野希美、水口賢司
    • Organizer
      CBI学会2013年大会 -生命医薬情報学連合大会-
    • Place of Presentation
      タワーホール船堀(東京都)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Enzyme function prediction using active sites and ligand binding sites information

    • Author(s)
      Chioko Nagao、Nozomi Nagano、Kenji Mizuguchi
    • Organizer
      第12回日本蛋白質科学会年会
    • Place of Presentation
      名古屋国際会議場(愛知)
    • Related Report
      2012 Research-status Report
  • [Presentation] Analysis of enzyme structures and functions/酵素の構造・機能の解析

    • Author(s)
      長野希美
    • Organizer
      BiWO2012
    • Place of Presentation
      産総研臨海副都心センター(東京)
    • Related Report
      2012 Research-status Report
  • [Remarks] ホームページ 等酵素反応データベース

    • URL

      http://mbs.cbrc.jp/EzCatDB/

    • Related Report
      2013 Final Research Report
  • [Remarks] 但し, 上記のドメイン名「mbs.cbrc.jp」が「ezcatdb.cbrc.jp」に変更になる可能性もある

    • Related Report
      2013 Final Research Report
  • [Remarks] 階層的酵素反応分類(RLCP)

    • URL

      http://mbs.cbrc.jp/EzCatDB/RLCP/

    • Related Report
      2013 Annual Research Report
  • [Remarks] 酵素反応データベース・EzCatDB

    • URL

      http://mbs.cbrc.jp/EzCatDB/

    • Related Report
      2012 Research-status Report
  • [Remarks] URL

    • URL

      http://mbs.cbrc.jp/EzCatDB/

    • Related Report
      2011 Research-status Report

URL: 

Published: 2011-08-05   Modified: 2019-07-29  

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