About: Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations

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An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://pubs.acs.org/doi/pdfplus/10.1021/ct400663s
Description	Hydrating water molecules are believed to be an inherent part of the RNA structure and have a considerable impact on RNA conformation. However, the magnitude and mechanism of the interplay between water molecules and the RNA structure are still poorly understood. In principle, such hydration effects can be studied by molecular dynamics (MD) simulations. In our recent MD studies, we observed that the choice of water model has a visible impact on the predicted structure and structural dynamics of RNA and, in particular, has a larger effect than type, parametrization, and concentration of the ions. Furthermore, the water model effect is sequence dependent and modulates the sequence dependence of A-RNA helical parameters. Clearly, the sensitivity of A-RNA structural dynamics to the water model parametrization is a rather spurious effect that complicates MD studies of RNA molecules. Hydrating water molecules are believed to be an inherent part of the RNA structure and have a considerable impact on RNA conformation. However, the magnitude and mechanism of the interplay between water molecules and the RNA structure are still poorly understood. In principle, such hydration effects can be studied by molecular dynamics (MD) simulations. In our recent MD studies, we observed that the choice of water model has a visible impact on the predicted structure and structural dynamics of RNA and, in particular, has a larger effect than type, parametrization, and concentration of the ions. Furthermore, the water model effect is sequence dependent and modulates the sequence dependence of A-RNA helical parameters. Clearly, the sensitivity of A-RNA structural dynamics to the water model parametrization is a rather spurious effect that complicates MD studies of RNA molecules. (en)
Title	Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations (en)
skos:prefLabel	Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations (en)
skos:notation	RIV/00216224:14740/14:00075656!RIV15-MSM-14740___
http://linked.open...avai/riv/aktivita	I P S
http://linked.open...avai/riv/aktivity	I, P(ED1.1.00/02.0068), P(ED2.1.00/03.0058), P(EE2.3.20.0017), P(GAP208/12/1878), P(GPP301/11/P558), S
http://linked.open...iv/cisloPeriodika	1
http://linked.open...vai/riv/dodaniDat	2015
http://linked.open...aciTvurceVysledku	Šponer, Jiří
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Masarykova univerzita / Středoevropský technologický institut
http://linked.open...dnocenehoVysledku	4080
http://linked.open...ai/riv/idVysledku	RIV/00216224:14740/14:00075656
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	AMBER FORCE-FIELD; LIQUID WATER; B-DNA; NUCLEIC-ACIDS; BIOMOLECULAR SIMULATIONS; POTENTIAL FUNCTIONS; SOLVATION DYNAMICS; AQUEOUS-SOLUTION; RIBOSOMAL-RNA; CHARGE MODEL (en)
http://linked.open.../riv/klicoveSlovo	POTENTIAL FUNCTIONS BIOMOLECULAR SIMULATIONS LIQUID WATER B-DNA AMBER FORCE-FIELD NUCLEIC-ACIDS AQUEOUS-SOLUTION RIBOSOMAL-RNA CHARGE MODEL SOLVATION DYNAMICS
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[89FA2C293C73]
http://linked.open...i/riv/nazevZdroje	Journal of Chemical Theory and Computation
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	4 (xsd:int)
http://linked.open...vavai/riv/projekt	Catalytic strategies of RNA and RNP enzymes studied by multi-scale computational approach Central european institute of technology Regional Centre of Advanced Technologies and Materials Research team development of the Regional Centre of Advanced Technologies and Materials Mechanism of catalytical self-cleavage of two non-coding RNAs of human patogens
http://linked.open...UplatneniVysledku	2014
http://linked.open...v/svazekPeriodika	10
http://linked.open...iv/tvurceVysledku	Otyepka, Michal Šponer, Jiří Banáš, Pavel Kuehrova, Petra
http://linked.open...ain/vavai/riv/wos	000330142400038
issn	1549-9618
number of pages	11 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/ct400663s
http://localhost/t...ganizacniJednotka	14740

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