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

Ayori Mitsutake; Hiromitsu Iijima; Hiroshi Takano

doi:10.1063/1.3652959

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

Ayori Mitsutake, Hiromitsu Iijima, Hiroshi Takano

Research output: Contribution to journal › Article › peer-review

33 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 language	English
Article number	164102
Journal	Journal of Chemical Physics
Volume	135
Issue number	16
DOIs	https://doi.org/10.1063/1.3652959
Publication status	Published - 2011 Oct 28
Externally published	Yes

ASJC Scopus subject areas

Physics and Astronomy(all)
Physical and Theoretical Chemistry

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10.1063/1.3652959

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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.",

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AU - Takano, Hiroshi

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

Abstract

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