• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Construction of Integrated Molecular Network Based on Interaction and Structural Information

Research Project

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
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥16,640,000 (Direct Cost: ¥12,800,000、Indirect Cost: ¥3,840,000)
Fiscal Year 2012: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2011: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2010: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2009: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Keywords分子ネットワーク / 相互作用 / 分子構造 / データベース / 構造
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.

Report

(5 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • 2009 Annual Research Report
  • Research Products

    (46 results)

All 2013 2012 2011 2010 2009 Other

All Journal Article (16 results) (of which Peer Reviewed: 16 results) Presentation (26 results) (of which Invited: 1 results) Remarks (4 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 Issue: 17 Pages: e129-e129

    • DOI

      10.1093/nar/gks462

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Analysis of Relationship among Evolvability, Thermodynamics and Function of Intrinsically Disordered Proteins/Regions2012

    • Author(s)
      H. He and A. Sarai
    • Journal Title

      Compt. Biol. Chem.

      Volume: 41 Pages: 51-57

    • Related Report
      2012 Annual Research Report
    • 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

    • Related Report
      2012 Final Research Report
    • 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: 8-8

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Analysis of electric moments of RNA-binding proteins : implications for mechanism and prediction2011

    • Author(s)
      S.Ahmad, A.Sarai
    • Journal Title

      BMC Struct.Biol.

      Volume: 11 Issue: 1 Pages: 8-8

    • DOI

      10.1186/1472-6807-11-8

    • Related Report
      2011 Annual Research Report
    • 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, S.Ahmad
    • Journal Title

      BMC Bioiformatics

      Volume: 12 Issue: S13

    • DOI

      10.1186/1471-2105-12-s13-s5

    • Related Report
      2011 Annual Research Report
    • 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

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] CCR XP : Exploring clusters of conserved residues in protein structures2010

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

      Nucleic Acids Res.

      Volume: 38

    • Related Report
      2010 Annual Research Report
    • 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

    • Related Report
      2012 Final Research Report
    • 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: 30-30

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] A signature-based method for indexing cell cycle phase distribution from microarray profiles2009

    • Author(s)
      H.Mizuno, Yo Nakanishi, N.Ishii, A.Sarai, K.Kitada
    • Journal Title

      BMC Genomics 10

      Pages: 137-137

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] PrognoScan : a new database for meta-analysis of the prognostic value of genes2009

    • Author(s)
      H.Mizuno, K.Kitada, K.Nakai, A.Sarai
    • Journal Title

      BMC Medical Genomics 2

      Pages: 18-18

    • Related Report
      2009 Annual Research Report
    • 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, S.Ahmad
    • Journal Title

      BMC Struct. Biol. 9

      Pages: 30-30

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] MHC class II DR classification based on antigen-binding groove natural selection2009

    • Author(s)
      S.Takeshima, A.Sarai, A.Saitou, Y.Aida
    • Journal Title

      Biochem. Biophys. Res.Comm. 385

      Pages: 137-142

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Generalized Conformational Energy Function of DNA Derived from Molecular Dynamics Simulations2009

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

      Nucleic Acids Res. 37

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Evaluation of DNA intramolecular interactions for nucleosome positioning in yeast2009

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

      Genome Inform. 23

      Pages: 13-20

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Presentation] Biophysics of molecular interaction network2013

    • Author(s)
      A. Sarai
    • Organizer
      The First BMIRC International Symposium on Frontiers in Computational Systems Biology and Bioengineering
    • Place of Presentation
      飯塚
    • Related Report
      2012 Annual Research Report
    • Invited
  • [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
    • Related Report
      2012 Annual Research Report 2012 Final Research Report
  • [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
    • Related Report
      2012 Annual Research Report 2012 Final Research Report
  • [Presentation] Integration of Structural and Biochemical Information into Protein Interaction Network2012

    • Author(s)
      Yuji Kawakami, Satoshi Fujii and Akinori Sarai
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Annual Research Report
  • [Presentation] Analysis of Domain and Non-Domain Interactions in Protein-Protein Interaction Network2012

    • Author(s)
      Satoshi Komori, Satoshi Fujii and Akinori Sarai
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Annual Research Report
  • [Presentation] The influence of solvent condition on DNA structures studied by molecular dynamics simulations2012

    • Author(s)
      Satoshi Fujii, Hidetoshi Kono and Akinori Sarai
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Annual Research Report
  • [Presentation] 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
    • Organizer
      European Conference on Computational Biology
    • Place of Presentation
      Basel, Switzerland
    • Related Report
      2012 Annual Research Report
  • [Presentation] Construction and Analysis of Protein-Protein Interaction Network Based on Domain and Non-Domain Interactions2011

    • Author(s)
      Satoshi Komori, Satoshi Fujii, Akinori Sarai
    • Organizer
      CBI/JSBi2011合同大会
    • Place of Presentation
      神戸
    • Related Report
      2011 Annual Research Report
  • [Presentation] Integration of Structural and Biochemical Information into Protein Interaction Network2011

    • Author(s)
      Yuji Kawakami, Satoshi Fujii, Akinori Sarai
    • Organizer
      CBI/JSBi2011合同大会
    • Place of Presentation
      神戸
    • Related Report
      2011 Annual Research Report
  • [Presentation] Construction and Analysis of Biomolecular Network in Structurome2010

    • Author(s)
      Yukari Hayashi, Satoshi Fujii, Akinori Sarai
    • Organizer
      第48回日本生物物理学会年会
    • Place of Presentation
      仙台
    • Related Report
      2010 Annual Research Report
  • [Presentation] Construction and Analysis of Biomolecular Network based on Domain Structures2010

    • Author(s)
      Yukari Hayashi, Satoshi Fujii, Akinori Sarai
    • Organizer
      2010年日本バイオインフォマティクス学会年会
    • Place of Presentation
      福岡
    • Related Report
      2010 Annual Research Report
  • [Presentation] 生体分子の熱力学データと構造データの統合2009

    • Author(s)
      皿井明倫、Shaji Kumar
    • Organizer
      文科省統合データベースプロジェクトシンポジウム「データベースが拓くこれからのライフサイエンス」
    • Place of Presentation
      東京
    • Year and Date
      2009-06-12
    • Related Report
      2009 Annual Research Report
  • [Presentation] Protein-DNA Recognition Mechanism and Prediction2009

    • Author(s)
      A.Sarai
    • Organizer
      Albany 2009 : The 16th Conversation
    • Place of Presentation
      Albany, NY, USA
    • Related Report
      2009 Annual Research Report
  • [Presentation] Analysis of Biomolecular Network in Structurome2009

    • Author(s)
      M.Ohtsuaka, S.Fujii, Akinori Sarai
    • Organizer
      ISMB/ECCB 2009
    • Place of Presentation
      Skockholm, Sweden
    • Related Report
      2009 Annual Research Report
  • [Presentation] Stability, Dynamics and Cooperativity of Protein-DNA Interactions2009

    • Author(s)
      A.Sarai
    • Organizer
      International Symposium on Multi-Scale Dynamics of Protein Complex Formation and Function
    • Place of Presentation
      Tokyo
    • Related Report
      2009 Annual Research Report
  • [Presentation] Kinase Inhibition modeling by Proteometrics and docking analysis2009

    • Author(s)
      Michael Fernandez, Ahmad Shandar, Akinori Sarai
    • Organizer
      CBI-KSBSB Joint Conference
    • Place of Presentation
      Busan, Korea
    • Related Report
      2009 Annual Research Report
  • [Presentation] Evaluation of DNA intramolecular interactions for nucleosome positioning in yeast2009

    • Author(s)
      M.Fernandez, S.Fujii, H.Kono, A.Sarai
    • Organizer
      GIW2009
    • Place of Presentation
      Yokohama
    • Related Report
      2009 Annual Research Report
  • [Presentation] 未構造タンパク質の機能的進化的特性 : 生物種特異的解析2009

    • Author(s)
      黄鶴、皿井明倫
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Related Report
      2009 Annual Research Report
  • [Presentation] ストラクチュロームにおける分子ネットワークの系統的解析2009

    • Author(s)
      Mitsuaki Ohtsuaka, Satoshi Fujii, Akinori Sarai
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Related Report
      2009 Annual Research Report
  • [Presentation] 転写因子のゲノムスケールでのターゲット予測 : 相互作用情報を用いた方法2009

    • Author(s)
      大庭宏明、藤井聡、皿井明倫
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Related Report
      2009 Annual Research Report
  • [Presentation] The effect of environment on the conformational transition of DNA studied by molecular dynamics simulations2009

    • Author(s)
      Satoshi Fujii, Hidetoshi Kono, Nobuhiro Go, Akinori Sarai
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Related Report
      2009 Annual Research Report
  • [Presentation] Construction and Analysis of Biomolecular Network based on Domain Structures2009

    • Author(s)
      Yukari Hayashi, Satoshi Fujii, Akinori Sarai
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Related Report
      2009 Annual Research Report
  • [Presentation] Motif Analysis of Transcription Factors in Regulatory Region2009

    • Author(s)
      T.Sakai, S.Fujii, A.Sarai
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Related Report
      2009 Annual Research Report
  • [Presentation] 構造情報に基づく蛋白質・DNA認識における協同性の解析2009

    • Author(s)
      A.Tanaka, S.Fujii, H.Kono, A.Sarai
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Related Report
      2009 Annual Research Report
  • [Presentation] ベイズ統計学的解釈によるタンパク質-DNA認識におけるindirect readoutの評価2009

    • Author(s)
      山崎智, 福井一彦, 河野秀俊, 清水謙多郎, 皿井明倫, 寺田透
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Related Report
      2009 Annual Research Report
  • [Presentation] Kinase Inhibition modeling by Proteometrics and docking analysis2009

    • Author(s)
      Michael Fernandez, Ahmad Shandar, Akinori Sarai
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      徳島
    • Related Report
      2009 Annual Research Report
  • [Remarks]

    • URL

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

    • Related Report
      2012 Final Research Report
  • [Remarks] PDBnet

    • URL

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

    • Related Report
      2012 Annual Research Report
  • [Remarks]

    • URL

      http://gibk26.bio.kyutech.ac.jp/jouhou/website/index.htm

    • Related Report
      2010 Annual Research Report
  • [Remarks]

    • URL

      http://gibk26.bse.kyutech.ac.jp/jouhou/website/index.htm

    • Related Report
      2009 Annual Research Report

URL: 

Published: 2009-04-01   Modified: 2019-07-29  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi