About: Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	The RNA hairpin loops represent important RNA topologies with indispensable biological functions in RNA folding and tertiary interactions. Explicit solvent molecular dynamics (MD) simulation is a computational technique which can efficiently complement the experimental data and provide unique structural dynamics information on the atomic scale. Nevertheless, outcome of simulations is often compromised by imperfections in parameterization of simplified pair-wise additive empirical potentials referred also as force fields. We have pointed out in several recent studies that force field description of single stranded hairpin segments of nucleic acids may be particularly challenging for the force fields. In this paper, we report a critical assessment of a broad set of MD simulations of UUCG, GAGA, and GAAA tetraloops using various force fields. The RNA hairpin loops represent important RNA topologies with indispensable biological functions in RNA folding and tertiary interactions. Explicit solvent molecular dynamics (MD) simulation is a computational technique which can efficiently complement the experimental data and provide unique structural dynamics information on the atomic scale. Nevertheless, outcome of simulations is often compromised by imperfections in parameterization of simplified pair-wise additive empirical potentials referred also as force fields. We have pointed out in several recent studies that force field description of single stranded hairpin segments of nucleic acids may be particularly challenging for the force fields. In this paper, we report a critical assessment of a broad set of MD simulations of UUCG, GAGA, and GAAA tetraloops using various force fields. (en)
Title	Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins (en)
skos:prefLabel	Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins (en)
skos:notation	RIV/68081707:_____/10:00373426!RIV12-GA0-68081707
http://linked.open...avai/riv/aktivita	P S Z
http://linked.open...avai/riv/aktivity	P(ED2.1.00/03.0058), P(GA203/09/1476), P(GD203/09/H046), P(IAA400040802), P(LC06030), P(LC512), S, Z(AV0Z50040507), Z(AV0Z50040702), Z(MSM6198959216)
http://linked.open...iv/cisloPeriodika	12
http://linked.open...vai/riv/dodaniDat	2012
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	Biofyzikální ústav AV ČR, v. v. i.
http://linked.open...dnocenehoVysledku	278491
http://linked.open...ai/riv/idVysledku	RIV/68081707:_____/10:00373426
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	molecular dynamics; force fields; RNA; tetraloops (en)
http://linked.open.../riv/klicoveSlovo	RNA molecular dynamics force fields tetraloops
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[EF30EA49D838]
http://linked.open...i/riv/nazevZdroje	Journal of Chemical Theory and Computation
http://linked.open...in/vavai/riv/obor	BO
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	8 (xsd:int)
http://linked.open...vavai/riv/projekt	Regional Centre of Advanced Technologies and Materials Biomolecular centre Center for biomolecules and complex molecular systems Structural dynamics, molecular interactions and function of key RNA motifs Biochemistry on the crossroad from in silico to in vitro Structure, dynamics, and reaction mechanism of catalytic RNA
http://linked.open...UplatneniVysledku	2010
http://linked.open...v/svazekPeriodika	6
http://linked.open...iv/tvurceVysledku	Šponer, Jiří Cheatham III, T. E. Otyepka, M. Banáš, P. Jurečka, P. Zgarbová, M. Orozco, M. Hollas, D.
http://linked.open...ain/vavai/riv/wos	000285217000019
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 Modulation of signalling and regulatory pathways in normal and cancer cells
issn	1549-9618
number of pages	14 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/ct100481h
is http://linked.open...avai/riv/vysledek of	Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins

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