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Tertiary structure prediction by multi-scale simulation

Research Project

Project/Area Number 23700359
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Bioinformatics/Life informatics
Research InstitutionNational Institute of Advanced Industrial Science and Technology

Principal Investigator

KAMEDA Tomoshi  独立行政法人産業技術総合研究所, 生命情報工学研究センター, 主任研究員 (40415774)

Project Period (FY) 2011 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2012: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2011: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Keywords蛋白質 / RNA / 立体構造予測 / 分子動力学(MD) / 分子動力学
Research Abstract

We developed the coarse-grained model of RNA molecule. Our model consists of 3 type beads(P: Phosphate, S: sugar, B: Base). Using this model, we carried out molecular dynamics simulation of RNA, which predicted native tertiary structure correctly.

Report

(3 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Research-status Report
  • Research Products

    (8 results)

All 2012 2011

All Journal Article (3 results) (of which Peer Reviewed: 3 results) Presentation (5 results)

  • [Journal Article] Lanthanide-assisted NMR evaluation of a dynamic ensemble of oligosaccharide conformations.2012

    • Author(s)
      S.Yamamoto, Y.Zhang, T.Yamaguchi, T.Kameda, and K.Kato
    • Journal Title

      Chem. Commun.

      Volume: 48 Issue: 39 Pages: 4752-4754

    • DOI

      10.1039/c2cc30353a

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] On easy implementation of a variant of the replica exchange with solute tempering in GROMACS2011

    • Author(s)
      T. Terakawa, T. Kameda, S. Takada
    • Journal Title

      J. Comp.Chem

      Volume: vol.32, No.7 Issue: 7 Pages: 1228-1234

    • DOI

      10.1002/jcc.21703

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Combined Use of Replica-Exchange Molecular Dynamics and Magic-Angle-Spinning Solid-State NMR Spectral Simulations for Determining the Structure and Orientation of Membrane-Bound Peptide2011

    • Author(s)
      Keisuke Ikeda, Tomoshi Kameda, Erisa Harada, Hideo Akutsu, and Toshimichi Fujiwara
    • Journal Title

      J. Phys. Chem. B

      Volume: 115 Issue: 29 Pages: 9327-9336

    • DOI

      10.1021/jp205290t

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Presentation] 粗視化モデル分子動力学法を用いた RNA 立体構造予測2012

    • Author(s)
      亀田倫史
    • Organizer
      日本生物物理学会
    • Place of Presentation
      名古屋大学(愛知県)
    • Year and Date
      2012-09-24
    • Related Report
      2012 Final Research Report
  • [Presentation] 粗視化モデル分子動力学法を用いたRNA 立体構造予測2012

    • Author(s)
      亀田倫史
    • Organizer
      日本生物物理学会
    • Place of Presentation
      名古屋大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] 分子動力学シミュレーション技術による化合物可溶化メカニズムの解明2012

    • Author(s)
      亀田倫史
    • Organizer
      CBI学会(招待講演)
    • Place of Presentation
      東京・総評会館
    • Related Report
      2011 Research-status Report
  • [Presentation] NMRと分子動力学法との融合2011

    • Author(s)
      亀田倫史
    • Organizer
      第12回若手NMR研究会(招待講演)
    • Place of Presentation
      滋賀・琵琶湖リゾートクラブ
    • Related Report
      2011 Research-status Report
  • [Presentation] 蛋白質異常凝集の原理と制御2011

    • Author(s)
      亀田倫史
    • Organizer
      大阪大学蛋白質研究所・蛋白研セミナー(招待講演)
    • Place of Presentation
      大阪・大阪大学蛋白質研究所
    • Related Report
      2011 Research-status Report

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Published: 2011-08-05   Modified: 2019-07-29  

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