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2012 Fiscal Year Final Research Report

Construction of Integrated Molecular Network Based on Interaction and Structural Information

Research Project

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Project/Area Number 21310131
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field ゲノム情報科学
Research InstitutionKyushu Institute of Technology

Principal Investigator

SARAI Akinori  九州工業大学, 大学院・情報工学研究院, 教授 (20221286)

Co-Investigator(Kenkyū-buntansha) FUJII Satoshi  九州工業大学, 大学院・情報工学研究院, 助教 (40452825)
Project Period (FY) 2009 – 2012
Keywords分子ネットワーク / 相互作用 / 分子構造 / データベース
Research Abstract

We have developed an integrated database/tool of biomolecular network, PDBnet, based on the structural and interaction information, in order to get useful information from the structurome. We have developed various interfaces for searching data and visualizing the results, which enables users to get insight into the relationship among structure, interaction, network and function of molecules. Using the data in PDBnet, we have made systematic analyses on the relationship among various properties at molecular structure, interaction and network levels to demonstrated the utility of PDBnet.

  • Research Products

    (9 results)

All 2012 2011 2010 2009 Other

All Journal Article (6 results) (of which Peer Reviewed: 6 results) Presentation (2 results) Remarks (1 results)

  • [Journal Article] A New Method for Evaluating the Specificity of Indirect Readout in Protein-DNA Recognition2012

    • Author(s)
      S. Yamasaki, T. Terada, H. Kono, K. Shimizu and A. Sarai
    • Journal Title

      Nucleic Acids Res

      Volume: 40 Pages: e129

    • DOI

      DOI:10.1093/nar/gks462

    • Peer Reviewed
  • [Journal Article] Prediction of dinucleotide-specific RNA-binding Sites in Proteins2011

    • Author(s)
      M. Fernandez, Y. Kumagai, D. Standley, K. Mizuguchi, A. Sarai and S. Ahmad
    • Journal Title

      BMC Bioiformatics 12(Suppl 13)

      Volume: S5

    • Peer Reviewed
  • [Journal Article] Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction2011

    • Author(s)
      H. Okayama, T. Kohno, Y. Ishii, Y. Shimada,S. Ahmad and A. Sarai
    • Journal Title

      BMC Struct. Biol

      Volume: 11 Pages: 8

    • Peer Reviewed
  • [Journal Article] CCR XP: Exploring clusters of conserved residues in protein structures2010

    • Author(s)
      S. Ahmad, O. Keskin, K. Mizuguchi, A. Sarai and R. Nussinov
    • Journal Title

      Nucleic Acids Res

      Volume: 38

    • Peer Reviewed
  • [Journal Article] Evaluation of DNA intramolecular interactions for nucleosome positioning in yeast2009

    • Author(s)
      M. Fernandez, S. Fujii, H. Kono and A. Sarai
    • Journal Title

      Genome Inform.

      Volume: 23 Pages: 13-20

    • Peer Reviewed
  • [Journal Article] Prediction of mono- and dinucleotide-specific DNA- binding sites in proteins using neural networks2009

    • Author(s)
      M. Andrabi, K. Mizuguchi, A. Sarai and S. Ahmad
    • Journal Title

      BMC Struct. Biol

      Volume: 9 Pages: 30

    • Peer Reviewed
  • [Presentation] Integration of Structural and Biochemical Information into Protein Interaction Network2012

    • Author(s)
      Yuji Kawakami, Satoshi Fujii and Akinori Sarai
    • Organizer
      生命医薬情報学連合大会
    • Place of Presentation
      東京
    • Year and Date
      20121014-17
  • [Presentation] Analysis of Domain and Non-Domain Interactions in Protein-Protein Interaction Network2012

    • Author(s)
      Satoshi Komori, Satoshi Fujii and Akinori Sarai
    • Organizer
      生命医薬情報学連合大会
    • Place of Presentation
      東京
    • Year and Date
      20121014-17
  • [Remarks]

    • URL

      http://www.abren.net/pdbnet/

URL: 

Published: 2014-08-29  

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