Principal component analysis and long time protein dynamics

M. A. Balsera, W. Wriggers, Y. Oono, K. Schulten

Research output: Contribution to journalArticle

Abstract

It has been suggested that principal component analysis can identify slow modes in proteins and, thereby, facilitate the study of long time dynamics. However, sampling errors due to finite simulation times preclude the identification of slow modes that can be used for this purpose. This is demonstrated numerically with the aid of simulations of the protein G-actin and analytically with the aid of a model which is exactly recoverable by principal component analysis. Although principal component analysis usually demonstrates that a set of a small number of modes captures the majority of the fluctuations, the set depends on the particular sampling time window and its width.

Original languageEnglish (US)
Pages (from-to)2567-2572
Number of pages6
JournalJournal of physical chemistry
Volume100
Issue number7
DOIs
StatePublished - Feb 15 1996

ASJC Scopus subject areas

  • Engineering(all)
  • Physical and Theoretical Chemistry

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    Balsera, M. A., Wriggers, W., Oono, Y., & Schulten, K. (1996). Principal component analysis and long time protein dynamics. Journal of physical chemistry, 100(7), 2567-2572. https://doi.org/10.1021/jp9536920