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Bioinformatics analysis of transition metal-binding proteins

Research Project

Project/Area Number 19500255
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionNara Institute of Science and Technology (2008-2009)
Japan Atomic Energy Agency (2007)

Principal Investigator

NAKAMURA Kensuke  Nara Institute of Science and Technology, 情報科学研究科, 特任准教授 (20212095)

Project Period (FY) 2007 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2009: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2008: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2007: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Keywords金属タンパク質 / ゲノム / 生命情報学 / 酵素 / 進化 / メタローム / 金属結合タンパク質 / メタロミクス / 分子進化 / 遷移金属イオン / 配列解析 / データベース / タンパク質 / 遷移金属 / 構造ゲノミクス
Research Abstract

Some of the transition metal ions such as iron, copper and zinc are known to be essential for life. Most of these transition metal ions in biological systems are functioning as complexes with specific metal binding proteins. The emergence of the terms such as metallome and metallomics, is indicating the increasing interest toward these metal binding proteins. Under such a circumstance, where a useful public bioinformatics resource for metal binding proteins is being desired, we have developed a new database system called MetalMine, which includes structural information of metal binding sites in an organized fashon. MetalMine is the largest database concerning metal binding proteins, in terms of the number of metal binding sites included, and it would serve as a quite useful resource for the functional analysis of proteins.

Report

(4 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • Research Products

    (22 results)

All 2010 2009 2008 2007 Other

All Journal Article (13 results) (of which Peer Reviewed: 13 results) Presentation (7 results) Remarks (2 results)

  • [Journal Article] a database of functional metal-binding sites in proteins2009

    • Author(s)
      K. Nakamura, A. Hirai, Md. Altaf-U1-Amin, H. Takahashi (4名1番目)" MetalMine
    • Journal Title

      Plant Biotechnology vol.26

      Pages: 517-521

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Metabolic pathway prediction based on inclusive relation between cyclic substructures2009

    • Author(s)
      K. Tanaka, K. Nakamura, T. Saito, H. Osada, A. Hirai, H. Takahashi, S. Kanaya, Md. Altaf Ul-Amin, (8名2番目)
    • Journal Title

      Plant Biotechnology vol.26

      Pages: 459-468

    • NAID

      10026136375

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Predicting conformation of protein complexes by determining statistically significant domain-domain interactions2009

    • Author(s)
      K. Nishikata, M. Wada, H. Takahashi, K. Nakamura, S. Kanaya, Md. Altaf-Ul-Amin, (6名4番目
    • Journal Title

      Plant Biotechnology vol.26

      Pages: 495-501

    • NAID

      10026136491

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] A Synthetic study on gymnastatins F and Q: the tandem Michael and aldol reaction approach2009

    • Author(s)
      K. Murayama, T. Tanabe, Y. Ishikawa, K. Nakamura, S. Nishiyama, (5名4番目)
    • Journal Title

      Tetrahedron Letters vol.50

      Pages: 3191-3194

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Anapproach to peak detection in GC-MS chromatograms and application of KNApSAcK database in prediction of candidate metabolites2009

    • Author(s)
      T. Oishi, (他16名12番目)
    • Journal Title

      Plant Biotechnology vol.26

      Pages: 167-174

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] MetalMine : a database of functional metal-binding sites in proteins2009

    • Author(s)
      K.Nakamura, A.Hirai, Md.Altaf-Ul-Amin, H.Takahashi
    • Journal Title

      Plant Biotechnology 26

      Pages: 517-521

    • NAID

      10026136588

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Metabolic pathway prediction based on inclusive relation between cyclic substructures2009

    • Author(s)
      K.Tanaka, K.Nakamura, T.Saito, H.Osada, A.Hirai, H.Takahashi, S.Kanaya, Md.Altaf-Ul-Amin
    • Journal Title

      Plant Biotechnology 26

      Pages: 459-468

    • NAID

      10026136375

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Predicting conformation of protein complexes by determining statisitically significant domain-domain interactions2009

    • Author(s)
      K.Nishikata, M.Wada, H.Takahashi, K.Nakamura S.Kanaya, Md.Altaf-Ul-Amin
    • Journal Title

      Plant Biotechnology 26

      Pages: 495-501

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Synthetic Study on Gymnastatins F and Q : The Tandem Michael and Aldol Reaction Approach2009

    • Author(s)
      K. Murayama
    • Journal Title

      Tetrahedron Letters 50(印刷中)

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] An approach to peak detection in GC-MS chromatograms and application of KNApSAcK database in prediction of candidate metabolites2009

    • Author(s)
      T. Oishi
    • Journal Title

      Plant biotechnology 26

      Pages: 167-174

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Synthesisi of pingusane-type sesquiterpenoids, acutifolone A and pinguisenol along with bisacutifolones through the Diels-Alder dimerization reaction2007

    • Author(s)
      J. Shiina, M. Oikawa, K. Nakamura, R. Obata, S. Nishiyama (5名3番目)
    • Journal Title

      European Journal of Organic Chemistry vol.2007

      Pages: 5190-5197

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] BAAQ: An Infrastructure for Application Integration and Knowledge Discovery in Bioinformatics2007

    • Author(s)
      G. Xiujun, K. Nakamura, H. Yu, K. Yura, N. Go, (5名2番目)
    • Journal Title

      IEEE Transactions on Information Technology in Biomedicine vol.11

      Pages: 428-434

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] BAAQ:An Infrastructure for Application Intergration and Knowledge Discovery in Bioinformatics2007

    • Author(s)
      Gong Xiujun, K. Nakamura, et. al.
    • Journal Title

      IEEE Transaction on Information Technology in Biomedicine 11

      Pages: 428-434

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Presentation] Metallome in coordination with Metabolome2010

    • Author(s)
      K. Nakamura, A. Hirai, H. Takahashi, S. Kanaya
    • Organizer
      8thMetabolome Informatics Workshop
    • Place of Presentation
      慶応鶴岡キャンパス
    • Year and Date
      2010-01-29
    • Related Report
      2009 Final Research Report
  • [Presentation] Metalome in coordination with Metabolome2010

    • Author(s)
      K.Nakamura, A.Hirai, H.Takahashi S.Kanaya
    • Organizer
      8th Metabolome Informatics Workshop
    • Place of Presentation
      慶応義塾鶴岡キャンパス(山形県)
    • Year and Date
      2010-01-29
    • Related Report
      2009 Annual Research Report
  • [Presentation] MetalMine: a databse of functional metal-ion-binding sites in proteins2009

    • Author(s)
      K. Nakamura, A. Hirai, H. Takahashi, Md. Altaf Ul-Amin, S. Kanaya
    • Organizer
      GIW2009 The 20th International Conference on Genome Informatics
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2009-12-15
    • Related Report
      2009 Final Research Report
  • [Presentation] MetalMine : a database of functional metal-ion-binding sites in proteins2009

    • Author(s)
      K.Nakamura, A.Hirai, H.Takahashi, Md.Altaf-Ul-Amin, S.Kanaya
    • Organizer
      The 20th International Conference on Genome Informatics
    • Place of Presentation
      パシフィコ横浜(神奈川県)
    • Year and Date
      2009-12-15
    • Related Report
      2009 Annual Research Report
  • [Presentation] 遷移金属結合サイトデータベースの構築2008

    • Author(s)
      中村建介
    • Organizer
      第八回日本タンパク質化学会年会
    • Place of Presentation
      タワーホール船堀(東京)
    • Year and Date
      2008-06-10
    • Related Report
      2009 Final Research Report
  • [Presentation] Prediction of Metal-Binding Sites for High-Throughput Metalloproteomics Data2007

    • Author(s)
      Kensuke Nakamura
    • Organizer
      VII European Symposium of The Protein Society
    • Place of Presentation
      ストックホルム/スヴェーデン
    • Year and Date
      2007-05-16
    • Related Report
      2007 Annual Research Report
  • [Presentation] Prediction of metal-binding sites for high-throughput metalloproteomics data2007

    • Author(s)
      K. Nakamura, K. Yura, N. Go
    • Organizer
      VII European Symposium of the Protein Society
    • Place of Presentation
      Stockholm, Sweden
    • Year and Date
      2007-05-15
    • Related Report
      2009 Final Research Report
  • [Remarks] 金属結合サイトデータベース:MetalMine

    • URL

      http://metalmine.naist.jp/metalmine009/index.html

    • Related Report
      2009 Final Research Report
  • [Remarks] MetalMine:タンパク質-金属イオン結合サイトデータベース

    • URL

      http://metalmine.naist.jp/

    • Related Report
      2009 Annual Research Report

URL: 

Published: 2007-04-01   Modified: 2016-04-21  

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