| Simulating DNA by molecular dynamics: aims, methods, and validation. | |
| | |
MedLine Citation:
|
PMID: 23034759 Owner: NLM Status: In-Data-Review |
Abstract/OtherAbstract:
|
The structure and dynamics of the B-DNA double helix involves subtle sequence-dependent effects which are decisive for its function, but difficult to characterize. These structural and dynamic effects can be addressed by simulations of DNA sequences in explicit solvent. Here, we present and discuss the state-of-art of B-DNA molecular dynamics simulations with the major force fields in use today. We explain why a critical analysis of the MD trajectories is required to assess their reliability, and estimate the value and limitations of these models. Overall, simulations of DNA bear great promise towards deciphering the structural and physical subtleties of this biopolymer, where much remains to be understood. |
| | |
Authors:
|
Nicolas Foloppe; Marc Guéroult; Brigitte Hartmann |
Related Documents
:
|
23578879 - Human evolution: turning back the clock. 8608899 - Ventromedial hypothalamic lesion-induced vagal hyperactivity stimulates rat pancreatic ... 23024359 - Zinc-binding domain of the bacteriophage t7 dna primase modulates binding to the dna te... 1934259 - Cellular levels of o6-methylguanine-dna methyltransferase in mammary epithelial cells a... 6196799 - Circadian rhythms of rna, dna and protein in the rat thyroid, adrenal and testis in chr... 23350029 - Equilibrious strand exchange promoted by dna conformational switching. 21533049 - Oligomerization of the e. coli core rna polymerase: formation of (α(2)ββ'ω)(2)-dna ... 6200339 - Chromatin structure, dna synthesis and transcription through the lifespan of human embr... 6084519 - Bleomycin may be activated for dna cleavage by nadph-cytochrome p-450 reductase. |
Publication Detail:
|
Type: Journal Article |
Journal Detail:
|
Title: Methods in molecular biology (Clifton, N.J.) Volume: 924 ISSN: 1940-6029 ISO Abbreviation: Methods Mol. Biol. Publication Date: 2013 |
Date Detail:
|
Created Date: 2012-10-04 Completed Date: - Revised Date: - |
Medline Journal Info:
|
Nlm Unique ID: 9214969 Medline TA: Methods Mol Biol Country: United States |
Other Details:
|
Languages: eng Pagination: 445-68 Citation Subset: IM |
Affiliation:
|
, Cambridge, UK. |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
|
|
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: Simulations of lipid monolayers.
Next Document: Simulation of carbohydrates, from molecular docking to dynamics in water.