Relaxation mode analysis of a peptide system: Comparison with principal component analysis

Ayori Mitsutake, Hiromitsu Iijima, Hiroshi Takano

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

This article reports the first attempt to apply the relaxation mode analysis method to a simulation of a biomolecular system. In biomolecular systems, the principal component analysis is a well-known method for analyzing the static properties of fluctuations of structures obtained by a simulation and classifying the structures into some groups. On the other hand, the relaxation mode analysis has been used to analyze the dynamic properties of homopolymer systems. In this article, a long Monte Carlo simulation of Met-enkephalin in gas phase has been performed. The results are analyzed by the principal component analysis and relaxation mode analysis methods. We compare the results of both methods and show the effectiveness of the relaxation mode analysis.

Original languageEnglish
Article number164102
JournalJournal of Chemical Physics
Volume135
Issue number16
DOIs
Publication statusPublished - 2011 Oct 28

Fingerprint

principal components analysis
Principal Component Analysis
Principal component analysis
peptides
Methionine Enkephalin
Peptides
Homopolymerization
Gases
simulation
classifying
dynamic characteristics
vapor phases
Monte Carlo simulation

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry
  • Medicine(all)

Cite this

Relaxation mode analysis of a peptide system : Comparison with principal component analysis. / Mitsutake, Ayori; Iijima, Hiromitsu; Takano, Hiroshi.

In: Journal of Chemical Physics, Vol. 135, No. 16, 164102, 28.10.2011.

Research output: Contribution to journalArticle

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