Parameter Evaluation and Test Application for FMO-DPD Simulation of Proteins

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  • TACHINO Yusuke
    Department of Chemistry, Rikkyo University (Nishi-Ikebukuro 3-34-1, Toshima-ku, Tokyo, 171-8501, Japan)
  • DOI Hideo
    Department of Chemistry, Rikkyo University (Nishi-Ikebukuro 3-34-1, Toshima-ku, Tokyo, 171-8501, Japan)
  • OKUWAKI Koji
    Department of Chemistry, Rikkyo University (Nishi-Ikebukuro 3-34-1, Toshima-ku, Tokyo, 171-8501, Japan) JSOL Corporation (Kudan-kaikan Terrace, Kudan-minami 1-6-5, Chiyoda-ku, Tokyo 102-0074, Japan)
  • HIRANO Yoshinori
    Graduate School of Science and Technology, Keio University (Hiyoshi 3-14-1, Kohoku-ku, Yokohama 223-8522, Japan)
  • MOCHIZUKI Yuji
    Department of Chemistry, Rikkyo University (Nishi-Ikebukuro 3-34-1, Toshima-ku, Tokyo, 171-8501, Japan) Institute of Industrial Science, The University of Tokyo (Komaba 4-6-1, Meguro-ku, Tokyo, 153-8505, Japan)

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  • タンパク質に関する FMO-DPD シミュレーション用パラメータ算定と試行

Abstract

<p>We have been promoting a project to evaluate the set of effective interaction parameters used in dissipative particle dynamics (DPD) simulations for all amino acid residues covering various proteins, based on fragment molecular orbital (FMO) calculations. This simulation protocol has been termed FMO-DPD. Here we report a test application to the folding problem of Chignolin and Superchignolin with hairpin structures, where 7 amino acid residues were considered.</p>

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