Easy Not Easy: Comparative Modeling with High-Sequence Identity Templates.
Comparative modeling
Conformational diversity
Conformational ensemble
Homology modeling
Native state
Protein dynamics
Protein structure
Structural divergence
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:
2023
2023
Historique:
entrez:
24
3
2023
pubmed:
25
3
2023
medline:
28
3
2023
Statut:
ppublish
Résumé
Homology modeling is the most common technique to build structural models of a target protein based on the structure of proteins with high-sequence identity and available high-resolution structures. This technique is based on the idea that protein structure shows fewer changes than sequence through evolution. While in this scenario single mutations would minimally perturb the structure, experimental evidence shows otherwise: proteins with high conformational diversity impose a limit of the paradigm of comparative modeling as the same protein sequence can adopt dissimilar three-dimensional structures. These cases present challenges for modeling; at first glance, they may seem to be easy cases, but they have a complexity that is not evident at the sequence level. In this chapter, we address the following questions: Why should we care about conformational diversity? How to consider conformational diversity when doing template-based modeling in a practical way?
Identifiants
pubmed: 36959443
doi: 10.1007/978-1-0716-2974-1_5
doi:
Substances chimiques
Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
83-100Informations de copyright
© 2023. Springer Science+Business Media, LLC, part of Springer Nature.
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