Non-Markov state model of peptide dynamics

Dmitry Nerukh

doi:10.1016/j.molliq.2012.06.011

Non-Markov state model of peptide dynamics

Dmitry Nerukh^*

^*Corresponding author for this work

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

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 language	English
Pages (from-to)	65-70
Number of pages	6
Journal	Journal of Molecular Liquids
Volume	176
Early online date	7 Jul 2012
DOIs	https://doi.org/10.1016/j.molliq.2012.06.011
Publication status	Published - Dec 2012

Keywords

conformational transitions
Markov state model
non-Markov
protein dynamics

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10.1016/j.molliq.2012.06.011

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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.",

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AB - 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.

KW - conformational transitions

KW - Markov state model

KW - non-Markov

KW - protein dynamics

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DO - 10.1016/j.molliq.2012.06.011

M3 - Article

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VL - 176

SP - 65

EP - 70

JO - Journal of Molecular Liquids

JF - Journal of Molecular Liquids

ER -

Non-Markov state model of peptide dynamics

Abstract

Keywords

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