Non-Markov state model of peptide dynamics

Dmitry Nerukh*

*Corresponding author for this work

Research output: Contribution to journalArticle

Abstract

A hidden Markov state model has been applied to classical molecular dynamics simulated small peptide in explicit water. The methodology allows increasing the time resolution of the model and describe the dynamics with the precision of 0.3 ps (comparing to 6 ps for the standard methodology). It also permits the investigation of the mechanisms of transitions between the conformational states of the peptide. The detailed description of one of such transitions for the studied molecule is presented.

Original languageEnglish
Pages (from-to)65-70
Number of pages6
JournalJournal of Molecular Liquids
Volume176
Early online date7 Jul 2012
DOIs
Publication statusPublished - Dec 2012

Keywords

  • conformational transitions
  • Markov state model
  • non-Markov
  • protein dynamics

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