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Statements

Subject Item
n2:RIV%2F68081707%3A_____%2F10%3A00373426%21RIV12-GA0-68081707
rdf:type
n15:Vysledek skos:Concept
dcterms: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. 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.
dcterms:title
Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins
skos:prefLabel
Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins
skos:notation
RIV/68081707:_____/10:00373426!RIV12-GA0-68081707
n3:aktivita
n7:S n7:P n7:Z
n3:aktivity
P(ED2.1.00/03.0058), P(GA203/09/1476), P(GD203/09/H046), P(IAA400040802), P(LC06030), P(LC512), S, Z(AV0Z50040507), Z(AV0Z50040702), Z(MSM6198959216)
n3:cisloPeriodika
12
n3:dodaniDat
n4:2012
n3:domaciTvurceVysledku
n13:3223779
n3:druhVysledku
n11:J
n3:duvernostUdaju
n14:S
n3:entitaPredkladatele
n19:predkladatel
n3:idSjednocenehoVysledku
278491
n3:idVysledku
RIV/68081707:_____/10:00373426
n3:jazykVysledku
n18:eng
n3:klicovaSlova
molecular dynamics; force fields; RNA; tetraloops
n3:klicoveSlovo
n6:tetraloops n6:RNA n6:force%20fields n6:molecular%20dynamics
n3:kodStatuVydavatele
US - Spojené státy americké
n3:kontrolniKodProRIV
[EF30EA49D838]
n3:nazevZdroje
Journal of Chemical Theory and Computation
n3:obor
n12:BO
n3:pocetDomacichTvurcuVysledku
1
n3:pocetTvurcuVysledku
8
n3:projekt
n8:IAA400040802 n8:LC06030 n8:LC512 n8:GA203%2F09%2F1476 n8:GD203%2F09%2FH046 n8:ED2.1.00%2F03.0058
n3:rokUplatneniVysledku
n4:2010
n3:svazekPeriodika
6
n3:tvurceVysledku
Cheatham III, T. E. Jurečka, P. Šponer, Jiří Hollas, D. Otyepka, M. Zgarbová, M. Banáš, P. Orozco, M.
n3:wos
000285217000019
n3:zamer
n16:AV0Z50040507 n16:AV0Z50040702 n16:MSM6198959216
s:issn
1549-9618
s:numberOfPages
14
n9:doi
10.1021/ct100481h