About: Dependence of A-RNA simulations on the choice of the force field and salt strength

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	We carried out an extensive molecular dynamics study on three A-RNA duplexes. Dependence of the A-RNA geometry on force fields (Parm99 and Parmbsc0) and salt strength conditions was investigated. The Parmbsc0 force field makes the A-RNA duplex more compact in comparison to the Parm99 by preventing temporary alpha/gamma t/t flips common in Parm99 simulations. The stabilization of the A-RNA helices caused by the Parmbsc0 force field includes visible reduction of the major groove width, increase of the base pair roll, larger helical inclination and small increases of twist. Therefore, the Parmbsc0 shifts the simulated duplexes more deeply into the A-form. We carried out an extensive molecular dynamics study on three A-RNA duplexes. Dependence of the A-RNA geometry on force fields (Parm99 and Parmbsc0) and salt strength conditions was investigated. The Parmbsc0 force field makes the A-RNA duplex more compact in comparison to the Parm99 by preventing temporary alpha/gamma t/t flips common in Parm99 simulations. The stabilization of the A-RNA helices caused by the Parmbsc0 force field includes visible reduction of the major groove width, increase of the base pair roll, larger helical inclination and small increases of twist. Therefore, the Parmbsc0 shifts the simulated duplexes more deeply into the A-form. (en)
Title	Dependence of A-RNA simulations on the choice of the force field and salt strength Dependence of A-RNA simulations on the choice of the force field and salt strength (en)
skos:prefLabel	Dependence of A-RNA simulations on the choice of the force field and salt strength Dependence of A-RNA simulations on the choice of the force field and salt strength (en)
skos:notation	RIV/68081707:_____/09:00333332!RIV10-MSM-68081707
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(1QS500040581), P(GD203/09/H046), P(IAA400040802), P(KJB400040901), P(LC06030), P(LC512), Z(AV0Z50040507), Z(AV0Z50040702), Z(MSM0021622413), Z(MSM6198959216)
http://linked.open...iv/cisloPeriodika	45
http://linked.open...vai/riv/dodaniDat	2010
http://linked.open...aciTvurceVysledku	Šponer, Jiří Beššeová, Ivana Réblová, Kamila Otyepka, Michal
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	Biofyzikální ústav AV ČR, v. v. i.
http://linked.open...dnocenehoVysledku	309474
http://linked.open...ai/riv/idVysledku	RIV/68081707:_____/09:00333332
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	force fileds; RNA; A-form (en)
http://linked.open.../riv/klicoveSlovo	force fileds RNA A-form
http://linked.open...odStatuVydavatele	GB - Spojené království Velké Británie a Severního Irska
http://linked.open...ontrolniKodProRIV	[9528FFF3958D]
http://linked.open...i/riv/nazevZdroje	Physical Chemistry Chemical Physics
http://linked.open...in/vavai/riv/obor	BO
http://linked.open...ichTvurcuVysledku	4 (xsd:int)
http://linked.open...cetTvurcuVysledku	4 (xsd:int)
http://linked.open...vavai/riv/projekt	Metallodrugs, design and mechansim of action Biomolecular centre Center for biomolecules and complex molecular systems Biochemistry on the crossroad from in silico to in vitro Structure, dynamics, and reaction mechanism of catalytic RNA Computational study of RNA multiple junctions localized in functionally important sites of the ribosome
http://linked.open...UplatneniVysledku	2009
http://linked.open...v/svazekPeriodika	11
http://linked.open...iv/tvurceVysledku	Beššeová, Ivana Otyepka, Michal Réblová, Kamila Šponer, Jiří
http://linked.open...ain/vavai/riv/wos	000271907200016
http://linked.open...n/vavai/riv/zamer	Biophysics of dynamic structures and functions of biological systems Genome and epigenome: 1D and 3D Structure, Dynamics, Interactions with Proteins and Functions Proteiny v metabolismu a při interakci organismů s prostředím Modulation of signalling and regulatory pathways in normal and cancer cells
issn	1463-9076
number of pages	11 (xsd:int)
is http://linked.open...avai/riv/vysledek of	Dependence of A-RNA simulations on the choice of the force field and salt strength Dependence of A-RNA simulations on the choice of the force field and salt strength Dependence of A-RNA simulations on the choice of the force field and salt strength Dependence of A-RNA simulations on the choice of the force field and salt strength

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