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Statements

Subject Item
n2:RIV%2F00216224%3A14740%2F14%3A00075659%21RIV15-MSM-14740___
rdf:type
n8:Vysledek skos:Concept
rdfs:seeAlso
http://pubs.acs.org/doi/pdfplus/10.1021/ct400837p
dcterms:description
Sugar-phosphate backbone is an electronically complex molecular segment imparting RNA molecules high flexibility and architectonic heterogeneity necessary for their biological functions. The structural variability of RNA molecules is amplified by the presence of the 2'-hydroxyl group, capable of forming multitude of intra- and intermolecular interactions. Bioinformatics studies based on X-ray structure database revealed that RNA backbone samples at least 46 substates known as rotameric families. The present study provides a comprehensive analysis of RNA backbone conformational preferences and 2'-hydroxyl group orientations. First, we create a benchmark database of estimated CCSD(T)/CBS relative energies of all rotameric families and test performance of dispersion-corrected DFT-D3 methods and molecular mechanics in vacuum and in continuum solvent. The performance of the DFT-D3 methods is in general quite satisfactory. Sugar-phosphate backbone is an electronically complex molecular segment imparting RNA molecules high flexibility and architectonic heterogeneity necessary for their biological functions. The structural variability of RNA molecules is amplified by the presence of the 2'-hydroxyl group, capable of forming multitude of intra- and intermolecular interactions. Bioinformatics studies based on X-ray structure database revealed that RNA backbone samples at least 46 substates known as rotameric families. The present study provides a comprehensive analysis of RNA backbone conformational preferences and 2'-hydroxyl group orientations. First, we create a benchmark database of estimated CCSD(T)/CBS relative energies of all rotameric families and test performance of dispersion-corrected DFT-D3 methods and molecular mechanics in vacuum and in continuum solvent. The performance of the DFT-D3 methods is in general quite satisfactory.
dcterms:title
Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations
skos:prefLabel
Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations
skos:notation
RIV/00216224:14740/14:00075659!RIV15-MSM-14740___
n3:aktivita
n18:P n18:I
n3:aktivity
I, P(ED1.1.00/02.0068), P(ED2.1.00/03.0058), P(EE2.3.20.0017), P(GAP208/12/1878)
n3:cisloPeriodika
1
n3:dodaniDat
n4:2015
n3:domaciTvurceVysledku
n7:3223779
n3:druhVysledku
n14:J
n3:duvernostUdaju
n13:S
n3:entitaPredkladatele
n15:predkladatel
n3:idSjednocenehoVysledku
14575
n3:idVysledku
RIV/00216224:14740/14:00075659
n3:jazykVysledku
n19:eng
n3:klicovaSlova
DENSITY-FUNCTIONAL THEORY; SUGAR-PHOSPHATE BACKBONE; QUANTUM-CHEMICAL CALCULATIONS; WATSON-CRICK/SUGAR-EDGE; GAUSSIAN-BASIS SETS; ACID BASE-PAIRS; GENERALIZED GRADIENT APPROXIMATION; CORRELATED MOLECULAR CALCULATIONS; NONEMPIRICAL AB-INITIO
n3:klicoveSlovo
n10:NONEMPIRICAL%20AB-INITIO n10:QUANTUM-CHEMICAL%20CALCULATIONS n10:GENERALIZED%20GRADIENT%20APPROXIMATION n10:DENSITY-FUNCTIONAL%20THEORY n10:CORRELATED%20MOLECULAR%20CALCULATIONS n10:GAUSSIAN-BASIS%20SETS n10:ACID%20BASE-PAIRS n10:SUGAR-PHOSPHATE%20BACKBONE n10:WATSON-CRICK%2FSUGAR-EDGE
n3:kodStatuVydavatele
US - Spojené státy americké
n3:kontrolniKodProRIV
[D5B413C39CD3]
n3:nazevZdroje
Journal of Chemical Theory and Computation
n3:obor
n11:CF
n3:pocetDomacichTvurcuVysledku
1
n3:pocetTvurcuVysledku
6
n3:projekt
n5:ED1.1.00%2F02.0068 n5:ED2.1.00%2F03.0058 n5:EE2.3.20.0017 n5:GAP208%2F12%2F1878
n3:rokUplatneniVysledku
n4:2014
n3:svazekPeriodika
10
n3:tvurceVysledku
Jurečka, Petr Zgarbová, Marie Otyepka, Michal Banáš, Pavel Šponer, Jiří Mládek, Arnošt
n3:wos
000330142400044
s:issn
1549-9618
s:numberOfPages
18
n20:doi
10.1021/ct400837p
n9:organizacniJednotka
14740