Folding simulation of small proteins by dissipative particle dynamics (DPD) with non-empirical interaction parameters based on fragment molecular orbital calculations

Koji Okuwaki, Hideo Doi, Kaori Fukuzawa, Yuji Mochizuki

研究成果: Article査読

5 被引用数 (Scopus)

抄録

Recently, we have developed a new simulation scheme with dissipative particle dynamics (DPD) based on non-empirical interaction parameters derived from a series of fragment molecular orbital (FMO) calculations. This approach (FMO-DPD) was applied to folding simulations of Chignolin and Superchignolin mini-proteins. Their characteristic hairpin structure was obtained from an elongated form within short computation time. Essential residue-residue interactions such as hydrogen bonding and CH/π were observed at the final form. FMO-DPD should have a potential applicability to nano-bio systems involving proteins.

本文言語English
論文番号017002
ジャーナルApplied Physics Express
13
1
DOI
出版ステータスPublished - 2020 1月 1
外部発表はい

ASJC Scopus subject areas

  • 工学(全般)
  • 物理学および天文学(全般)

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