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Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature
We apply the non-Markov-type analysis of state-to-state transitions to nearly microsecond molecular dynamics (MD) simulation data at a folding temperature of a small artificial protein, chignolin, and we found that the time scales obtained are consistent with our previous result using the weighted e...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9410030/ https://www.ncbi.nlm.nih.gov/pubmed/36013367 http://dx.doi.org/10.3390/life12081188 |
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author | Fujisaki, Hiroshi Suetani, Hiromichi Maragliano, Luca Mitsutake, Ayori |
author_facet | Fujisaki, Hiroshi Suetani, Hiromichi Maragliano, Luca Mitsutake, Ayori |
author_sort | Fujisaki, Hiroshi |
collection | PubMed |
description | We apply the non-Markov-type analysis of state-to-state transitions to nearly microsecond molecular dynamics (MD) simulation data at a folding temperature of a small artificial protein, chignolin, and we found that the time scales obtained are consistent with our previous result using the weighted ensemble simulations, which is a general path-sampling method to extract the kinetic properties of molecules. Previously, we also applied diffusion map (DM) analysis, which is one of a manifold of learning techniques, to the same trajectory of chignolin in order to cluster the conformational states and found that DM and relaxation mode analysis give similar results for the eigenvectors. In this paper, we divide the same trajectory into shorter pieces and further apply DM to such short-length trajectories to investigate how the obtained eigenvectors are useful to characterize the conformational change of chignolin. |
format | Online Article Text |
id | pubmed-9410030 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-94100302022-08-26 Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature Fujisaki, Hiroshi Suetani, Hiromichi Maragliano, Luca Mitsutake, Ayori Life (Basel) Article We apply the non-Markov-type analysis of state-to-state transitions to nearly microsecond molecular dynamics (MD) simulation data at a folding temperature of a small artificial protein, chignolin, and we found that the time scales obtained are consistent with our previous result using the weighted ensemble simulations, which is a general path-sampling method to extract the kinetic properties of molecules. Previously, we also applied diffusion map (DM) analysis, which is one of a manifold of learning techniques, to the same trajectory of chignolin in order to cluster the conformational states and found that DM and relaxation mode analysis give similar results for the eigenvectors. In this paper, we divide the same trajectory into shorter pieces and further apply DM to such short-length trajectories to investigate how the obtained eigenvectors are useful to characterize the conformational change of chignolin. MDPI 2022-08-03 /pmc/articles/PMC9410030/ /pubmed/36013367 http://dx.doi.org/10.3390/life12081188 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Fujisaki, Hiroshi Suetani, Hiromichi Maragliano, Luca Mitsutake, Ayori Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature |
title | Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature |
title_full | Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature |
title_fullStr | Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature |
title_full_unstemmed | Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature |
title_short | Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature |
title_sort | non-markov-type analysis and diffusion map analysis for molecular dynamics trajectory of chignolin at a high temperature |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9410030/ https://www.ncbi.nlm.nih.gov/pubmed/36013367 http://dx.doi.org/10.3390/life12081188 |
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