Extracting the Dynamic Motion of Proteins Using Normal Mode Analysis.
Computational chemistry
Conformational analysis
Elastic network model
Molecular dynamics
Normal mode analysis
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:
2022
2022
Historique:
entrez:
4
5
2022
pubmed:
5
5
2022
medline:
7
5
2022
Statut:
ppublish
Résumé
Normal mode analysis (NMA) is a technique for describing the conformational states accessible to a protein in a minimum energy conformation. NMA gives results similar to those produced by principal components analysis of a molecular dynamics simulation, but with only a fraction of the computational effort. Here, we provide a brief overview of the theory and describe three methods for carrying out NMA, including the use of one of the on-line services, the use of off-line software for calculating the projection of the modes calculated from one conformation onto another, and an all-atom NMA calculated using GROMACS. For all three methods, we will use the E1·2Ca
Identifiants
pubmed: 35507265
doi: 10.1007/978-1-0716-2095-3_9
doi:
Substances chimiques
Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
213-231Informations de copyright
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
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