RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F18%3A00492310" target="_blank" >RIV/68081707:_____/18:00492310 - isvavai.cz</a>
Alternative codes found
RIV/61989592:15310/18:73591542
Result on the web
<a href="https://pubs.acs.org/doi/10.1021/acs.chemrev.7b00427" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.chemrev.7b00427</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.chemrev.7b00427" target="_blank" >10.1021/acs.chemrev.7b00427</a>
Alternative languages
Result language
angličtina
Original language name
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
Original language description
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10608 - Biochemistry and molecular biology
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2018
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Chemical Reviews
ISSN
0009-2665
e-ISSN
1520-6890
Volume of the periodical
118
Issue of the periodical within the volume
8
Country of publishing house
US - UNITED STATES
Number of pages
162
Pages from-to
4177-4338
UT code for WoS article
000431095200004
EID of the result in the Scopus database
2-s2.0-85045378342