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in silico analysis of molecular interactions between commercially available drugs in Japan and proteins

Research Project

Project/Area Number 19200024
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionTokai University

Principal Investigator

HIRAYAMA Noriaki  Tokai University (70238393)

Co-Investigator(Kenkyū-buntansha) MUTA Hajime  東海大学, 医学部, 助教 (80384923)
Project Period (FY) 2007 – 2010
Project Status Completed (Fiscal Year 2010)
Budget Amount *help
¥26,390,000 (Direct Cost: ¥20,300,000、Indirect Cost: ¥6,090,000)
Fiscal Year 2010: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000)
Fiscal Year 2009: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000)
Fiscal Year 2008: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2007: ¥16,120,000 (Direct Cost: ¥12,400,000、Indirect Cost: ¥3,720,000)
Keywords医薬分子 / タンパク質 / 分子認識 / ドッキング / 分子力学
Research Abstract

Understanding of modes of interactions between drugs and proteins is important to promote drug discovery and studies on side-effects of drugs. Although it is not practically possible to measure all the interactions experimentally, in silico methods are expected to become viable alternatives. In this project, we have studied novel methodologies essential for this purpose, and applied them to evaluate the interactions between commercially available drugs and proteins which are closely related to carbohydrate metabolism.

Report

(6 results)
  • 2010 Annual Research Report   Final Research Report ( PDF )
  • 2009 Annual Research Report   Self-evaluation Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • Research Products

    (40 results)

All 2010 2009 2008 2007

All Journal Article (20 results) (of which Peer Reviewed: 20 results) Presentation (20 results)

  • [Journal Article] Use of aminoacid composition to predict epitope residues of indivisual antibodie2010

    • Author(s)
      S.Soga, D.Kuroda, H.Shirai, M.Koboriand N.Hiarayama
    • Journal Title

      Protein Eng.Des.Sel. 23

      Pages: 441-448

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] A noveltarget-based de novo ligand designby use of pseudomolecular probe2010

    • Author(s)
      K.Toda, J.Goto, N.Hirayama
    • Journal Title

      Med.Chem.Comm. 1

      Pages: 349-354

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Alpha Sphere Filter Method : Application of Pseudomolecular Descriptors in Virtual Screening of 2D Chemical Structures2010

    • Author(s)
      H.Muta, N.Hirayama
    • Journal Title

      J.Comput.Chem. 31

      Pages: 2225-2232

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Use of amino acid composition to predict epitope residues of individual antibodies2010

    • Author(s)
      S.Soga, D.Kuroda, H.Shirai, M.Kobori, N.Hiarayama
    • Journal Title

      Protein Eng Des Sel.

      Volume: 23 Pages: 441-448

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A novel target-based de novo ligand design by use of pseudomolecular probe2010

    • Author(s)
      K.Toda, J.Goto, N.Hirayama
    • Journal Title

      Med.Chem.Comm

      Volume: 1 Pages: 349-354

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Alpha Sphere Filter Method : Application of Pseudomolecular Descriptors in Virtual Screening of 2D Chemical Structures2010

    • Author(s)
      H.Muta, N.Hirayama
    • Journal Title

      J.Comput.Chem

      Volume: 31 Pages: 2225-2232

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Alpha Sphere Filter Method : Application of Pseudomolecular Descriptors in Virtual Screening of 2D Chemical Structures2010

    • Author(s)
      M. Muta, N. Hirayama
    • Journal Title

      J.Comput.Chem. 31

    • Related Report
      2009 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Use of amino acid composition to predict epitope residues of individual antibodies2010

    • Author(s)
      S. Soga, D. Kuroda, H. Shirai, M. Kobori, N. Hirayama
    • Journal Title

      Protein Eng.Des.Sel. 23

      Pages: 441-448

    • Related Report
      2009 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] 擬似分子プローブと標的分子構造に基づくde novo医薬分子設計法の開発2009

    • Author(s)
      東田欣也、後藤純一、平山令明
    • Journal Title

      SAR News 16

      Pages: 16-20

    • Related Report
      2010 Final Research Report 2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Chemocavity : specific concavity in protein reserved for the binding of biologically functional small molecules2008

    • Author(s)
      S.Soga, H.Shirai, M.Kobori, N.Hirayama
    • Journal Title

      J.Chem.Inf. Model. 48

      Pages: 1679-1685

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Use of Amino Acid Composition to Predict Ligand?Binding Sites2008

    • Author(s)
      N.Hirayama, S.Soga,H.Shirai, M.Kobori
    • Journal Title

      Drugs of the Future 33A

      Pages: 76-76

    • NAID

      130004574950

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] ASEDock-Docking Based on Alpha Spheres and Excluded Volumes2008

    • Author(s)
      J.Goto, R.Kataoka, H.Muta, N.Hirayama
    • Journal Title

      J.Chem.Inf.Model. 48

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Chemocavity : specific concavity in protein reserved for the binding of biologically functional small molecules2008

    • Author(s)
      S. Soga. H. Shirai, M. Kobori, N. Hiravama
    • Journal Title

      J.Chem.Inf. 48

      Pages: 1679-1685

    • Related Report
      2009 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Chemocavity : specific concavity in protein reserved for the binding of biologically functional small molecules2008

    • Author(s)
      S. Soga, H. Shirai, M. Kobori, N. Hirayama
    • Journal Title

      J. Chem. Inf. Model 48

      Pages: 1679-1685

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Use of Amino Acid Composition to Predict Ligand-Binding Sites2008

    • Author(s)
      N. Hirayama, S. Soga, H. Shirai, M. Kobori
    • Journal Title

      Drugs of the Future 33A

      Pages: 76-76

    • NAID

      130004574950

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] ASEDock-Docking Based on Alpha Spheres and Excluded Volumes2008

    • Author(s)
      J.Goto, R.Kataoka, H.Muta and N.Hirayama
    • Journal Title

      J.Chem.Inf.Model. 48(印刷中)

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identification of the druggable concavity in homology models using the PLB index2007

    • Author(s)
      S.Soga, H.Shirai, M.Kobori, N.Hirayama
    • Journal Title

      J.Chem.Inf.Model. 47

      Pages: 2287-2292

    • NAID

      130004574951

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Use of Amino Acid Composition to Predict Ligand-Binding Sites2007

    • Author(s)
      S.Soga, H.Shirai, M.Kobori, N.Hirayama
    • Journal Title

      J.Chem.Inf. Model. 47

      Pages: 400-406

    • NAID

      130004574950

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Identification of the druggable concavity in homology models using the PLB index2007

    • Author(s)
      S.Soga, H.Shirai, M.Kobori and N.Hirayama
    • Journal Title

      J.Chem.Inf.Model. 47

      Pages: 2287-2292

    • NAID

      130004574951

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Use of Amino Acid Composition to Predict Ligand-Binding Sites2007

    • Author(s)
      S.Soga, H.Shirai, M.Kobori and N.Hirayama
    • Journal Title

      J.Chem.Inf.Model. 47

      Pages: 400-406

    • NAID

      130004574950

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Presentation] コンピュータを用いた合理的創薬法の現状とその可能性2010

    • Author(s)
      平山令明
    • Organizer
      第25回日本整形外科学会基礎学術集会
    • Place of Presentation
      国立京都国際会館(京都)
    • Year and Date
      2010-10-15
    • Related Report
      2010 Annual Research Report 2010 Final Research Report
  • [Presentation] アミノ酸組成を利用した医薬分子結合部位の予測2010

    • Author(s)
      曽我真司、白井宏樹、小堀正人、平山令明
    • Organizer
      CBI学会2010年大会
    • Place of Presentation
      学術総合センター(東京)
    • Year and Date
      2010-09-16
    • Related Report
      2010 Annual Research Report 2010 Final Research Report
  • [Presentation] in silico創薬科学は稀少疾患治療薬の研究開発を可能にするか?2010

    • Author(s)
      平山令明
    • Organizer
      CBI学会2010年大会
    • Place of Presentation
      学術総合センター(東京)
    • Year and Date
      2010-09-15
    • Related Report
      2010 Annual Research Report 2010 Final Research Report
  • [Presentation] PLB法を用いた低分子結合部位の差別化2009

    • Author(s)
      平山令明
    • Organizer
      第10回日本バイオインフォマティクス学会創薬インフォマティクス研究会
    • Place of Presentation
      産総研臨海副都心センター(東京)
    • Year and Date
      2009-12-02
    • Related Report
      2010 Final Research Report
  • [Presentation] PLB法を用いた低分子結合部位の差別化2009

    • Author(s)
      平山令明
    • Organizer
      第10回日本バイオインフォマティクス学会
    • Place of Presentation
      木産業技術総合研究所 (東京)
    • Year and Date
      2009-12-02
    • Related Report
      2009 Self-evaluation Report
  • [Presentation] PLB法を用いた低分子結合部位の差別化2009

    • Author(s)
      平山令明
    • Organizer
      第10回 日本バイオインフォマティクス学会創薬インフォマティクス研究会
    • Place of Presentation
      産総研 臨海副都心センター (東京)
    • Year and Date
      2009-12-02
    • Related Report
      2009 Annual Research Report
  • [Presentation] AutoGPA:グリッドとファーマコフォアモデルの連携による3D-QSARモデルの自動構築2009

    • Author(s)
      朝川直行、小林誠一、後藤純一、平山令明
    • Organizer
      第37回構造活性相関シンポジウム
    • Place of Presentation
      北里大学薬学部(東京)
    • Year and Date
      2009-11-13
    • Related Report
      2009 Annual Research Report
  • [Presentation] AutoGPA モデルによる受容体ポケットの特徴抽出2009

    • Author(s)
      朝川直行、小林誠一、後藤純一、平山令明
    • Organizer
      第37回構造活性相関シンポジウム
    • Place of Presentation
      北里大学薬学部(東京)
    • Year and Date
      2009-11-12
    • Related Report
      2010 Final Research Report
  • [Presentation] AutoGPAモデルによる受容体ポケットの特徴抽出2009

    • Author(s)
      朝川直行、小林誠一、後藤純一、平山令明
    • Organizer
      第37回構造活性相関シンポジウム
    • Place of Presentation
      北里大学薬学部(東京)
    • Year and Date
      2009-11-12
    • Related Report
      2009 Annual Research Report
  • [Presentation] Chemocavity : Specific Concavity in Protein Reserved for the Binding of Biologically Functional Small Molecules2009

    • Author(s)
      S.Soga, H.Shirai, M.Kobori, N.Hirayama
    • Organizer
      17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 8th European Conference on Computational Biology (ECCB)
    • Place of Presentation
      ストックホルム、スウェーデン
    • Year and Date
      2009-07-01
    • Related Report
      2010 Final Research Report
  • [Presentation] Chemocavity : Specific concavity in protein reserved for the binding of biologically functional small molecules2009

    • Author(s)
      S. Soga, H. Shirai, M. Kobori, N. Hirayama
    • Organizer
      17th Annual International Conference on Intelligent Systems for Molecular Biology
    • Place of Presentation
      ストックホルム (スウェーデン)
    • Year and Date
      2009-07-01
    • Related Report
      2009 Self-evaluation Report
  • [Presentation] Chemocavity : Specific Concavity in Protein Reserved for the Binding of Biologically Functional Small Molecules2009

    • Author(s)
      S.Soga, H.Shirai, M.Kobori, N.Hirayama
    • Organizer
      17th Annual International Conference on Intelligent Systems for Molecular Biologv (ISMB) and 8th European Conference on Computational Biology (ECCB)
    • Place of Presentation
      Stockholm, Sweden
    • Year and Date
      2009-07-01
    • Related Report
      2009 Annual Research Report
  • [Presentation] アミノ酸の共起性から見た蛋白質の低分子化合物結合部位2008

    • Author(s)
      曽我真司,白井宏樹,小堀正人,平山令明
    • Organizer
      第36回構造活性相関シンポジウム
    • Place of Presentation
      神戸国際会議場(神戸)
    • Year and Date
      2008-11-03
    • Related Report
      2010 Final Research Report 2008 Annual Research Report
  • [Presentation] 疑似分子プローブと標的構造に基づくde novo医薬分子設計法の開発2008

    • Author(s)
      東田欣也, 後藤純一, 平山令明
    • Organizer
      第36回構造活性相関シンポジウム
    • Place of Presentation
      神戸国際会議場(神戸)
    • Year and Date
      2008-11-02
    • Related Report
      2008 Annual Research Report
  • [Presentation] Use of Amino Acid Composition to Predict Ligand-Binding Sites2008

    • Author(s)
      平山令明
    • Organizer
      XXth International Symposium on Medicinal Chemistry
    • Place of Presentation
      ウイーン(オーストリア)
    • Year and Date
      2008-09-04
    • Related Report
      2010 Final Research Report
  • [Presentation] Use of Amino Acid Composition to Predict Ligand-Bindine Sites2008

    • Author(s)
      平山令明
    • Organizer
      XXth International Symposium on Medicinal Chemistry
    • Place of Presentation
      ウイーン(オーストリア)
    • Year and Date
      2008-09-04
    • Related Report
      2008 Annual Research Report
  • [Presentation] アミノ酸の共起性から見た蛋白質の低分子化合物結合部位2008

    • Author(s)
      曽我真司,白井宏樹,小堀正人,平山令明
    • Organizer
      第8回日本蛋白質科学会年会
    • Place of Presentation
      タワーホール船堀(東京)
    • Year and Date
      2008-06-10
    • Related Report
      2010 Final Research Report 2008 Annual Research Report
  • [Presentation] アミノ酸組成を利用した医薬分子結合部位の予測2007

    • Author(s)
      曽我 真司, 白井 宏樹, 小堀 正人, 平山 令明
    • Organizer
      第30回情報化学討論会
    • Place of Presentation
      京都大学
    • Year and Date
      2007-11-16
    • Related Report
      2007 Annual Research Report
  • [Presentation] PLBを利用した蛋白質モデル構造における医薬分子結合部位の予測2007

    • Author(s)
      曽我 真司, 白井 宏樹, 小堀 正人, 平山 令明
    • Organizer
      第30回情報化学討論会
    • Place of Presentation
      京都大学
    • Year and Date
      2007-11-16
    • Related Report
      2007 Annual Research Report
  • [Presentation] In silico screening: from nice-to-use to must-use technology for drug discovery2007

    • Author(s)
      平山 令明
    • Organizer
      情報計算化学生物学会 2007年大会
    • Place of Presentation
      広島大学
    • Year and Date
      2007-10-05
    • Related Report
      2007 Annual Research Report

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

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