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Genome wide protein structure and function prediction database using homology modelling

Research Project

Project/Area Number 15013251
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionKitasato University

Principal Investigator

UMEYAMA Hideaki  Kitasato University, School of Pharmaceutical Sciences, Professor, 薬学部, 教授 (20050619)

Co-Investigator(Kenkyū-buntansha) IWADATE Mitsuo  Kitasato University, School of Pharmaceutical Sciences, Assistant Professor, 薬学部, 講師 (10327447)
NISHIKAWA Kwn  National Institute of Genetics, DDBJ research centre, Professor, 生命情報・DDBJ研究センター, 教授 (10093288)
FUKAMI Kaoru  RIKEN, Bio Resource centre, head of room, バイオリソースセンター, 室長 (20225494)
Project Period (FY) 2003 – 2004
Project Status Completed (Fiscal Year 2004)
Budget Amount *help
¥56,000,000 (Direct Cost: ¥56,000,000)
Fiscal Year 2004: ¥28,000,000 (Direct Cost: ¥28,000,000)
Fiscal Year 2003: ¥28,000,000 (Direct Cost: ¥28,000,000)
Keywordsprotein / structure / prediction / CASP / CAFASP / FAMS / GTOP / FAMSBASE / ゲノム / ホモロジーモデリング / コンピュータ解析 / アライメント / FAMS、FAMSBASE / バイオインフォマティックス / プロテオーム / 遺伝子 / タンパク質データベ-ス / タンパク質立体構造予測 / 機能進化解析
Research Abstract

Protein Structural Model database "FAMSBASE" was constructed using homology modeling program "FAMS".
And homology search results web site "GTOP" was constructed.
It is were available via
http://www.pharm.kitasato-u.ac.jp/fams/
http://spock.genes.nig.ac.jp/~genome/

Report

(3 results)
  • 2004 Annual Research Report   Final Research Report Summary
  • 2003 Annual Research Report
  • Research Products

    (25 results)

All 2005 2004 2003 Other

All Journal Article (18 results) Publications (7 results)

  • [Journal Article] A fully automated homology modeling system for protein-protein complex structure2005

    • Author(s)
      Mayuko Takeda-Shitaka, Genki Terashi, Chieko Chiba, Daisuke Takaya, Hideaki Umeyama
    • Journal Title

      Medicinal Chemistry (in press)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Protein structure prediction in CASP6 using CHIMERA and FAMS2005

    • Author(s)
      Mayuko Takeda-Shitaka, Genki Terashi, Daisuke Takaya, Kazuhiko Kanou, Mitsuo Iwadate, Hideaki Umeyama
    • Journal Title

      Proteins (Published on line)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Searching for protein-protein interaction sites and protein-protein docking by the methods of molecular dynamics, grid scoring and the pair-wise interaction potential of amino acid residues.2005

    • Author(s)
      Terashi G, Takeda-Shitaka M, Takaya D, Umeyama H
    • Journal Title

      Proteins 60

      Pages: 289-295

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Protein structure prediction in CASP6 using CHIMERA and FAMS2005

    • Author(s)
      Mayuko Takeda-Shitaka, Genki Terashi, Daisuke Takaya, Kazuhiko Kanou, Mitsuo Iwadate, Hideaki Umeyama
    • Journal Title

      Proteins Published online

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Searching for protein-protein interaction sites and protein-protein docking by the methods of molecular dynamics, grid scoring and the pair-wise interaction potential of amino acid residues.2005

    • Author(s)
      Terashi G, Takeda-Shitaka M, Takaya D, Umeyama H.
    • Journal Title

      Proteins 60

      Pages: 289-295

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Predicting absolute contact numbers of native protein structure from amino acid sequence.2005

    • Author(s)
      Kinjo, A.R., Horimoto, K., Nishikawa, K.
    • Journal Title

      Proteins 58

      Pages: 158-165

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Estimation of the number of authentic orphan genes in bacterial genomes.2004

    • Author(s)
      Fukukuchi, S., Nishikawa, K.
    • Journal Title

      DNA Res. 11

      Pages: 219-231

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Estimation of the number of authentic orphan genes in bacterial genomes.2004

    • Author(s)
      Fukukuchi, S., Nishikawa K.
    • Journal Title

      DNA Res. 11

      Pages: 219-231

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Remarkably different structures and reaction mechanisms of ketoreductases for the opposite stereochemical control in the biosynthesis of BIQ antibiotics.2004

    • Author(s)
      著者11人9番目に梅山秀明
    • Journal Title

      Bioorg Med Chem. 12

      Pages: 5917-5927

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Evaluation of homology modeling of the severe acute respiratory syndrome (SARS) coronavirus main protease for structure based drug design2004

    • Author(s)
      Takeda-Shitaka M, Nojima H, Takaya D, Kanou K, Iwadate M, Umeyama
    • Journal Title

      Chem Pharm Bull (Tokyo). 52

      Pages: 643-645

    • NAID

      110003615633

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Estimation of the number of authentic orphan genes in bacterial genomes2004

    • Author(s)
      Fukuchi, S., Nishikawa, K.
    • Journal Title

      DNA Res. 11

      Pages: 219-231

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Alternative splice variants encoding unstable protein domains exist in the human brain.2004

    • Author(s)
      Homma, K., Kikuno, R.F., Nagase, T., Ohara, O., Nishikawa, K.
    • Journal Title

      J.Mol.Biol. 343

      Pages: 1207-1220

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Integrative annotation of 21,037 human genes validated by full-length cDNA clones.2004

    • Author(s)
      著者多数、その中に西川健
    • Journal Title

      PLoS Biology 2

      Pages: 856-875

    • NAID

      120004667172

    • Related Report
      2004 Annual Research Report
  • [Journal Article] タンパク質から見た極限微生物の環境適応戦略2004

    • Author(s)
      吉宗一晃, 福地佐斗志, 森口光瞭, 西川健
    • Journal Title

      バイオサイエンスとインダストリー

      Pages: 6-6

    • NAID

      10016213588

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures.2003

    • Author(s)
      Nakashima, H., Fukuchi, S., Nishikawa, K.
    • Journal Title

      J. Biochem. 133

      Pages: 507-513

    • NAID

      130003534527

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Parallel Evolution of Ligand Specificity Between LacI/GalR Family Repressors and Periplasmic Sugar-Binding Proteins.2003

    • Author(s)
      Fukami-Kobayashi K., Tateno, Y., Nishikawa, K.
    • Journal Title

      Mol. Biol. Evol. 20

      Pages: 267-277

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures.2003

    • Author(s)
      Nakashima, H., Fukuchi, S., Nishikawa K.
    • Journal Title

      J.Biochem. 133

      Pages: 207-513

    • NAID

      130003534527

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Parallel Evolution of Ligand Specificity Between LacI/GalR Family Repressors and Periplasmic Sugar-Binding Proteins.2003

    • Author(s)
      Fukami-Kobayashi K., Tateno, Y., Nishikawa K.
    • Journal Title

      Mol.Biol.Evol. 20

      Pages: 267-277

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Publications] Komatsu k., Kurihara Y, Iwadate M, Takeda-Shitaka M, Umeyama H: "Third Solvent Clusters Fitting for Protein-Protein Interaction Prediction"PROTEINS, Structure, Function and Genomics. 52・1. 15-18 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Adachi M, Kurihara Y, Nojima H, Takeda-Shitaka M, Kamiya K, Umeyama H: "Interaction between the antigen and antibody is controlled by the constant domains : Normal mode dynamics of the HEL-HyHEL-10 complex"Protein Science. 12・10. 2131-2135 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Fukuchi S, Yoshimune K, Wakayama M, Moriguchi M, Nishikawa K: "Unique amino acid composition of proteins in halophilic bactera"Journal of Molecular Biology. 327・4. 347-357 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Nakashima H, Fukuchi S, Nishikawa K: "Compositional Changes in RNA, DNA and Proteins for Bacterial Adaptation to Higher and Lower Temperatures"Journal of Biochemistry (Tokyo). 133・3. 507-513 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Ota M, Kinoshita K, Nishikawa K: "Prediction of Catalytic Residues in Enzymes Based on Known Tertiary Structure, Stability Profile, and Sequence Conservation"Journal of Molecular Biology. 327・5. 1053-1064 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Fukami-Kobayashi K, Tateno Y, Nishikawa K: "Parallel Evolution of Ligand Specificity Between LacI/GalR Family Repressors and Periplasmic Sugar-Binding Proteins"Molecular Biology and Evolution. 20・3. 267-277 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] 岩舘満雄, 梅山秀明(分担執筆): "ゲノム創薬 合理的創薬からテーラーメイド医療実現へ(田沼靖一編) タンパク質立体構造のホモロジーモデリング"化学同人(化学フロンティア(12)). 39-50 (2003)

    • Related Report
      2003 Annual Research Report

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Published: 2003-04-01   Modified: 2018-03-28  

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