This HTML5 document contains 60 embedded RDF statements represented using HTML+Microdata notation.

The embedded RDF content will be recognized by any processor of HTML5 Microdata.

Namespace Prefixes

PrefixIRI
dctermshttp://purl.org/dc/terms/
n14http://localhost/temp/predkladatel/
n20http://linked.opendata.cz/resource/domain/vavai/riv/tvurce/
n5http://linked.opendata.cz/resource/domain/vavai/projekt/
n11http://linked.opendata.cz/resource/domain/vavai/subjekt/
n10http://linked.opendata.cz/ontology/domain/vavai/
shttp://schema.org/
skoshttp://www.w3.org/2004/02/skos/core#
rdfshttp://www.w3.org/2000/01/rdf-schema#
n4http://linked.opendata.cz/ontology/domain/vavai/riv/
n8http://bibframe.org/vocab/
n13http://linked.opendata.cz/resource/domain/vavai/vysledek/RIV%2F00216224%3A14740%2F13%3A00068733%21RIV14-MSM-14740___/
n2http://linked.opendata.cz/resource/domain/vavai/vysledek/
rdfhttp://www.w3.org/1999/02/22-rdf-syntax-ns#
n12http://linked.opendata.cz/ontology/domain/vavai/riv/klicoveSlovo/
n19http://linked.opendata.cz/ontology/domain/vavai/riv/duvernostUdaju/
xsdhhttp://www.w3.org/2001/XMLSchema#
n18http://linked.opendata.cz/ontology/domain/vavai/riv/aktivita/
n9http://linked.opendata.cz/ontology/domain/vavai/riv/jazykVysledku/
n17http://linked.opendata.cz/ontology/domain/vavai/riv/druhVysledku/
n15http://linked.opendata.cz/ontology/domain/vavai/riv/obor/
n7http://reference.data.gov.uk/id/gregorian-year/

Statements

Subject Item
n2:RIV%2F00216224%3A14740%2F13%3A00068733%21RIV14-MSM-14740___
rdf:type
n10:Vysledek skos:Concept
rdfs:seeAlso
http://pubs.acs.org/doi/pdf/10.1021/ct301086z
dcterms:description
RNA hairpin loops represent important RNA motifs with indispensable biological functions in RNA folding and tertiary interactions, with the 5'-UNCG-3' and 5'-GNRA-3' families being the most abundant. Molecular dynamics simulations represent a powerful method to investigate the structure, folding, and function of these tetraloops (TLs), but previous AMBER force fields were unable to maintain even the native structure of small TL RNAs. Here, we have used Replica Exchange Molecular Dynamics (REMD) with our recent reparameterization of AMBER RNA force field to study the folding of RNA hairpins containing representatives UNCG and GNRA TLs. We find that in each case, we are able to reach conformations within 2 A of the native structure, in contrast to results with earlier force fields. RNA hairpin loops represent important RNA motifs with indispensable biological functions in RNA folding and tertiary interactions, with the 5'-UNCG-3' and 5'-GNRA-3' families being the most abundant. Molecular dynamics simulations represent a powerful method to investigate the structure, folding, and function of these tetraloops (TLs), but previous AMBER force fields were unable to maintain even the native structure of small TL RNAs. Here, we have used Replica Exchange Molecular Dynamics (REMD) with our recent reparameterization of AMBER RNA force field to study the folding of RNA hairpins containing representatives UNCG and GNRA TLs. We find that in each case, we are able to reach conformations within 2 A of the native structure, in contrast to results with earlier force fields.
dcterms:title
Computer Folding of RNA Tetraloops? Are We There Yet? Computer Folding of RNA Tetraloops? Are We There Yet?
skos:prefLabel
Computer Folding of RNA Tetraloops? Are We There Yet? Computer Folding of RNA Tetraloops? Are We There Yet?
skos:notation
RIV/00216224:14740/13:00068733!RIV14-MSM-14740___
n10:predkladatel
n11:orjk%3A14740
n4:aktivita
n18:P n18:I
n4:aktivity
I, P(ED1.1.00/02.0068), P(ED2.1.00/03.0058), P(EE2.3.20.0017), P(EE2.3.20.0058), P(GAP208/12/1878), P(GBP208/12/G016), P(GBP305/12/G034), P(GPP301/11/P558)
n4:cisloPeriodika
4
n4:dodaniDat
n7:2014
n4:domaciTvurceVysledku
n20:3223779
n4:druhVysledku
n17:J
n4:duvernostUdaju
n19:S
n4:entitaPredkladatele
n13:predkladatel
n4:idSjednocenehoVysledku
66583
n4:idVysledku
RIV/00216224:14740/13:00068733
n4:jazykVysledku
n9:eng
n4:klicovaSlova
MOLECULAR-DYNAMICS SIMULATIONS; SARCIN RICIN LOOP; FORCE-FIELD; RIBOSOMAL-RNA; ANGSTROM RESOLUTION; CRYSTAL-STRUCTURE; ENERGY LANDSCAPE; NUCLEIC-ACIDS; DNA HAIRPIN; TERTIARY INTERACTIONS
n4:klicoveSlovo
n12:DNA%20HAIRPIN n12:TERTIARY%20INTERACTIONS n12:ENERGY%20LANDSCAPE n12:MOLECULAR-DYNAMICS%20SIMULATIONS n12:FORCE-FIELD n12:ANGSTROM%20RESOLUTION n12:RIBOSOMAL-RNA n12:CRYSTAL-STRUCTURE n12:SARCIN%20RICIN%20LOOP n12:NUCLEIC-ACIDS
n4:kodStatuVydavatele
US - Spojené státy americké
n4:kontrolniKodProRIV
[25C3A2F6755E]
n4:nazevZdroje
Journal of Chemical Theory and Computation
n4:obor
n15:CF
n4:pocetDomacichTvurcuVysledku
1
n4:pocetTvurcuVysledku
5
n4:projekt
n5:EE2.3.20.0058 n5:EE2.3.20.0017 n5:GAP208%2F12%2F1878 n5:ED1.1.00%2F02.0068 n5:ED2.1.00%2F03.0058 n5:GPP301%2F11%2FP558 n5:GBP208%2F12%2FG016 n5:GBP305%2F12%2FG034
n4:rokUplatneniVysledku
n7:2013
n4:svazekPeriodika
9
n4:tvurceVysledku
Otyepka, Michal Best, Robert B. Banáš, Pavel Kuhrova, Petra Šponer, Jiří
n4:wos
000317438100025
s:issn
1549-9618
s:numberOfPages
11
n8:doi
10.1021/ct301086z
n14:organizacniJednotka
14740