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Statements

Subject Item
n2:RIV%2F00216224%3A14740%2F14%3A00076672%21RIV15-MSM-14740___
rdf:type
n16:Vysledek skos:Concept
rdfs:seeAlso
http://pubs.acs.org/doi/abs/10.1021/jz500557y
dcterms:description
We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation. We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation.
dcterms:title
Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome
skos:prefLabel
Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome
skos:notation
RIV/00216224:14740/14:00076672!RIV15-MSM-14740___
n3:aktivita
n13:P n13: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
10
n3:dodaniDat
n10:2015
n3:domaciTvurceVysledku
n12:6410715 n12:3223779
n3:druhVysledku
n6:J
n3:duvernostUdaju
n17:S
n3:entitaPredkladatele
n20:predkladatel
n3:idSjednocenehoVysledku
30283
n3:idVysledku
RIV/00216224:14740/14:00076672
n3:jazykVysledku
n7:eng
n3:klicovaSlova
DELTA-VIRUS RIBOZYME; AMBER FORCE-FIELD; REPLICA-EXCHANGE METHOD; SAM-II RIBOSWITCH; RNA KISSING-LOOP; STRUCTURAL DYNAMICS; QUADRUPLEX DNA; EXPLICIT SOLVENT; ENERGY LANDSCAPES; BINDING-SITES
n3:klicoveSlovo
n8:RNA%20KISSING-LOOP n8:REPLICA-EXCHANGE%20METHOD n8:BINDING-SITES n8:AMBER%20FORCE-FIELD n8:QUADRUPLEX%20DNA n8:DELTA-VIRUS%20RIBOZYME n8:STRUCTURAL%20DYNAMICS n8:ENERGY%20LANDSCAPES n8:SAM-II%20RIBOSWITCH n8:EXPLICIT%20SOLVENT
n3:kodStatuVydavatele
US - Spojené státy americké
n3:kontrolniKodProRIV
[78B92F707B0D]
n3:nazevZdroje
The Journal of Physical Chemistry Letters
n3:obor
n18:CF
n3:pocetDomacichTvurcuVysledku
2
n3:pocetTvurcuVysledku
9
n3:projekt
n9:EE2.3.20.0017 n9:ED1.1.00%2F02.0068 n9:ED2.1.00%2F03.0058 n9:GAP208%2F12%2F1878
n3:rokUplatneniVysledku
n10:2014
n3:svazekPeriodika
5
n3:tvurceVysledku
Banáš, Pavel Havrila, Marek Otyepka, Michal Šponer, Jiří Zgarbová, Marie Stadlbauer, Petr Kührová, Petra Krepl, Miroslav Jurečka, Petr
n3:wos
000336199000027
s:issn
1948-7185
s:numberOfPages
12
n19:doi
10.1021/jz500557y
n14:organizacniJednotka
14740