Performance of Molecular Mechanics Force Fields for RNA Simulations. Stability of UUCG and GNRA Hairpins

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F10%3A10215348" target="_blank" >RIV/61989592:15310/10:10215348 - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/10:00353763 RIV/68081707:_____/10:00373426
Result on the web
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DOI - Digital Object Identifier
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Result language
angličtina
Original language name
Performance of Molecular Mechanics Force Fields for RNA Simulations. Stability of UUCG and GNRA Hairpins
Original language description
The RNA hairpin loops represent important RNA topologies with indispensable biological functions in RNA folding and tertiary interactions. Explicit solvent molecular dynamics (MD) simulation is a computational technique which can efficiently complement the experimental data and provide unique structural dynamics information on the atomic scale. Nevertheless, outcome of simulations is often compromised by imperfections in parameterization of simplified pair-wise additive empirical potentials referred also as force fields. We have pointed out in several recent studies that force field description of single stranded hairpin segments of nucleic acids may be particularly challenging for the force fields. In this paper, we report a critical assessment of a broad set of MD simulations of UUCG, GAGA, and GAAA tetraloops using various force fields.
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>Z - Vyzkumny zamer (s odkazem do CEZ)<br>S - Specificky vyzkum na vysokych skolach

Publication year
2010
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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