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Comprehensive analysis of the structural information of disorder proteins using computers

Research Project

Project/Area Number 21500289
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionThe University of Tokyo

Principal Investigator

NAKAMURA Shugo  東京大学, 大学院・農学生命科学研究科, 准教授 (90272442)

Project Period (FY) 2009 – 2011
Project Status Completed (Fiscal Year 2011)
Budget Amount *help
¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
Fiscal Year 2011: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2010: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2009: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywordsコンピュータシミュレーション / ディスオーダー蛋白質 / ディスオーダー / 蛋白質 / 構造予測 / シミュレーション / 立体構造予測 / タンパク質 / 局所構造情報
Research Abstract

I have applied protein structure prediction method and molecular dynamics simulation to amino acid sequences of various intrinsically disordered regions/proteins(IDRs/IDPs). I found that these amino acid sequences include structural information as the same degree of loop regions of ordered proteins and that tertiary structures of some IDPs after complex formation are even predictable without information of partner proteins.

Report

(4 results)
  • 2011 Annual Research Report   Final Research Report ( PDF )
  • 2010 Annual Research Report
  • 2009 Annual Research Report
  • Research Products

    (20 results)

All 2012 2011 2010 2009

All Journal Article (12 results) (of which Peer Reviewed: 12 results) Presentation (8 results)

  • [Journal Article] Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates2012

    • Author(s)
      M. Morita, M. Kakuta, K. Shimizu, S. Nakamura
    • Journal Title

      J. Proteome Sci. Comput. Biol.

      Volume: 1

    • URL

      http://www.hoajonline.com/jpscb/1/1/1

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Prospects for tertiary structure prediction of RNA basea on secondary structure information2012

    • Author(s)
      S.Yamasaki, S.Nakamura, K.Fukui
    • Journal Title

      J.Chem.Inf.Model.

      Volume: 52 Issue: 2 Pages: 557-567

    • DOI

      10.1021/ci2003413

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Protein-protein docking using multi-layered spherical basis functions2011

    • Author(s)
      K. Sumikoshi, T. Terada, S. Nakamura, K. Shimizu
    • Journal Title

      Int. Proc. Chem., Biol. Environ. Eng.

      Volume: 5 Pages: 342-347

    • URL

      http://www.ipcbee.com/vol5/76-X10027.pdf

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] BUDDY-system : A web site for constructing a dataset of protein pairs between ligand-bound and unbound states2011

    • Author(s)
      M. Morita, T. Terada, S. Nakamura, K. Shimizu
    • Journal Title

      BMC Res. Notes

      Volume: 4 Issue: 1 Pages: 143-143

    • DOI

      10.1186/1756-0500-4-143

    • Related Report
      2011 Annual Research Report 2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Prediction of N-myristoylation modification of proteins by SVM2011

    • Author(s)
      W. Cao, K. Sumikoshi, S. Nakamura, T. Terada, K. Shimizu
    • Journal Title

      Bioinformation

      Volume: 6(5) Pages: 204-206

    • URL

      http://www.bioinformation.net/006/97320630006204.pdf

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Protein-protein docking using multi-layered spherical basis functions2011

    • Author(s)
      K.Sumikoshi, T.Terada, S.Nakamura, K.Shimizu
    • Journal Title

      Int.Proc.Chem., Biol.Environ.Eng.

      Volume: 5 Pages: 342-347

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Prediction of N-myristoylation modification of proteins by SVM2011

    • Author(s)
      W.Cao, K.Sumikoshi, S.Nakamura, T.Terada, K.Shimizu
    • Journal Title

      Bioinformation

      Volume: 6 Pages: 204-206

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mutually exclusive expression of Gaia and Ga14 reveals diversification of taste receptor cells in zebrafish2011

    • Author(s)
      M.Ohmoto, S.Okada, S.Nakamura, K.Abe, I.Matsumoto
    • Journal Title

      J.Comp.Neurol.

      Volume: 519 Issue: 8 Pages: 1616-1629

    • DOI

      10.1002/cne.22589

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Prediction of carbohydrate-binding proteins from sequences using support vector machines2010

    • Author(s)
      S. Someya, M. Kakuta, M. Morita, K. Sumikoshi, W. Cao, Z. Ge, O. Hirose, S. Nakamura, T. Terada, K. Shimizu
    • Journal Title

      Adv. Bioinform.

      Volume: 2010 Pages: 1-9

    • DOI

      10.1155/2010/289301

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Prediction of carbohydrate-binding proteins from sequences using support vector machines2010

    • Author(s)
      S.Someya, M.Kakuta, M.Morita, K. Sumikoshi, W.Cao, Z.Ge, O.Hirose, S.Nakamura, T.Terada, K.Shimizu
    • Journal Title

      Adv.Bioinform.

      Volume: ArticleID:289301

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Comprehensive analysis of sequence-structure relationships in the loop regions of proteins2009

    • Author(s)
      S. Nakamura, K. Shimizu
    • Journal Title

      Genome Inform.

      Volume: 23(1) Pages: 106-116

    • URL

      http://giw.hgc.jp/giw2009/pdf/33-Nakamura.pdf

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Comprehensive analysis of sequence-structure relationships in the loop regions of proteins2009

    • Author(s)
      中村周吾
    • Journal Title

      Genome Informatics 23

      Pages: 106-116

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Presentation] アミノ酸配列からのタンパク質立体構造予測と4次構造予測2011

    • Author(s)
      中村周吾
    • Organizer
      日本生化学会大会
    • Place of Presentation
      国立京都国際会館
    • Year and Date
      2011-09-23
    • Related Report
      2011 Final Research Report
  • [Presentation] アミノ酸配列からのタンパク質立体構造予測と4次構造予測2011

    • Author(s)
      中村周吾
    • Organizer
      第84回日本生化学会大会シンポジウム
    • Place of Presentation
      国立京都国際会館(招待講演)
    • Year and Date
      2011-09-23
    • Related Report
      2011 Annual Research Report
  • [Presentation] 蛋白質のホモマー構造予測2011

    • Author(s)
      中村周吾
    • Organizer
      計算タンパク質科学研究会
    • Place of Presentation
      伊良湖
    • Year and Date
      2011-08-30
    • Related Report
      2011 Annual Research Report 2011 Final Research Report
  • [Presentation] Bilab in CASP9-モノマーおよび複合体構造予測-2011

    • Author(s)
      中村周吾
    • Organizer
      IPAB公開セミナーCASP9特集
    • Place of Presentation
      東京工業大学
    • Year and Date
      2011-02-24
    • Related Report
      2011 Final Research Report
  • [Presentation] Bilab in CASP9~モノマーおよび複合体構造予測~2011

    • Author(s)
      中村周吾
    • Organizer
      IPAB公開セミナーCASP9特集
    • Place of Presentation
      東京工業大学
    • Year and Date
      2011-02-24
    • Related Report
      2010 Annual Research Report
  • [Presentation] 蛋白質モデル構造の品質評価について2010

    • Author(s)
      中村周吾
    • Organizer
      計算タンパク質科学研究会
    • Place of Presentation
      城崎大会議館
    • Year and Date
      2010-09-04
    • Related Report
      2011 Final Research Report 2010 Annual Research Report
  • [Presentation] Development of protein local structure prediction method based on combination of multiple support vector machines2009

    • Author(s)
      中村周吾
    • Organizer
      生物物理学会年会
    • Place of Presentation
      アスティとくしま
    • Year and Date
      2009-10-30
    • Related Report
      2011 Final Research Report 2009 Annual Research Report
  • [Presentation] タンパク質の局所配列構造相関について2009

    • Author(s)
      中村周吾
    • Organizer
      計算タンパク質科学研究会
    • Place of Presentation
      聴泉閣かめや
    • Year and Date
      2009-09-03
    • Related Report
      2011 Final Research Report 2009 Annual Research Report

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Published: 2009-04-01   Modified: 2016-04-21  

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