Are waters around RNA more than just a solvent? An insight from molecular dynamics simulations.

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F14%3A33152189" target="_blank" >RIV/61989592:15310/14:33152189 - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/14:00428669 RIV/00216224:14740/14:00075656
Result on the web
<a href="http://pubs.acs.org/doi/pdf/10.1021/ct400663s" target="_blank" >http://pubs.acs.org/doi/pdf/10.1021/ct400663s</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/ct400663s" target="_blank" >10.1021/ct400663s</a>

Result language
angličtina
Original language name
Are waters around RNA more than just a solvent? An insight from molecular dynamics simulations.
Original language description
Hydrating water molecules are believed to be an inherent part of the RNA structure and have a considerable impact on RNA conformation. However, the magnitude and mechanism of the interplay between water molecules and the RNA structure are still poorly understood. In principle, such hydration effects can be studied by molecular dynamics (MD) simulations. In our recent MD studies, we observed that the choice of water model has a visible impact on the predicted structure and structural dynamics of RNA and,in particular, has a larger effect than type, parametrization, and concentration of the ions. Furthermore, the water model effect is sequence dependent and modulates the sequence dependence of A-RNA helical parameters. Clearly, the sensitivity of A-RNAstructural dynamics to the water model parametrization is a rather spurious effect that complicates MD studies of RNA molecules. These results nevertheless suggest that the sequence dependence of the A-RNA structure, usually attributed to
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
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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)<br>S - Specificky vyzkum na vysokych skolach

Publication year
2014
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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