Design and simulation of DNA, RNA and hybrid protein-nucleic acid nanostructures with oxView.
Journal
Nature protocols
ISSN: 1750-2799
Titre abrégé: Nat Protoc
Pays: England
ID NLM: 101284307
Informations de publication
Date de publication:
08 2022
08 2022
Historique:
received:
13
07
2021
accepted:
18
01
2022
pubmed:
7
6
2022
medline:
6
8
2022
entrez:
6
6
2022
Statut:
ppublish
Résumé
Molecular simulation has become an integral part of the DNA/RNA nanotechnology research pipeline. In particular, understanding the dynamics of structures and single-molecule events has improved the precision of nanoscaffolds and diagnostic tools. Here we present oxView, a design tool for visualization, design, editing and analysis of simulations of DNA, RNA and nucleic acid-protein nanostructures. oxView provides an accessible software platform for designing novel structures, tweaking existing designs, preparing them for simulation in the oxDNA/RNA molecular simulation engine and creating visualizations of simulation results. In several examples, we present procedures for using the tool, including its advanced features that couple the design capabilities with a coarse-grained simulation engine and scripting interface that can programmatically edit structures and facilitate design of complex structures from multiple substructures. These procedures provide a practical basis from which researchers, including experimentalists with limited computational experience, can integrate simulation and 3D visualization into their existing research programs.
Identifiants
pubmed: 35668321
doi: 10.1038/s41596-022-00688-5
pii: 10.1038/s41596-022-00688-5
doi:
Substances chimiques
Nucleic Acids
0
RNA
63231-63-0
DNA
9007-49-2
Types de publication
Journal Article
Review
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
1762-1788Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer Nature Limited.
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