Enhanced Molecular Dynamics Simulations of Intrinsically Disordered Proteins.
Collective variables
Molecular dynamics
NTAIL
Replica Exchange
Well-Tempered Ensemble
Well-tempered metadynamics
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2020
2020
Historique:
entrez:
23
7
2020
pubmed:
23
7
2020
medline:
11
3
2021
Statut:
ppublish
Résumé
Molecular dynamics simulations represent a powerful tool to gain insights into structural and dynamical features of biomolecular systems. Nevertheless, their recognized limitation in terms of achievable timescales becomes particularly severe when dealing with slow processes. In such cases, the employment of enhanced sampling methods, which allow accelerating the characterization of rare events in a timeframe consistent with conventional computational resources, results as crucial. In particular, such advanced techniques have proven highly valuable in the context of protein folding and, specifically, to explore the conformational ensemble spanned by intrinsically disordered proteins (IDPs). Here, we describe how to set up molecular dynamics simulations with one of these enhanced sampling approaches (namely, Parallel Tempering Metadynamics in the Well-Tempered Ensemble) using the N
Identifiants
pubmed: 32696368
doi: 10.1007/978-1-0716-0524-0_19
doi:
Substances chimiques
Intrinsically Disordered Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
391-411Références
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