About: Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations

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About: Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations Goto Sponge NotDistinct Permalink

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	RNA molecules are stabilized by a wide range of noncanonical interactions that are not present in DNA. Among them, the recently classified base phosphate (BPh) interactions belong to the most important ones. Twelve percent of nucleotides in the ribosomal crystal structures are involved in BPh interactions. Here we provide assessment of the energetics of BPh interactions using MP2 computations extrapolated to the complete basis set of atomic orbitals and corrected for higher-order electron correlation effects. RNA molecules are stabilized by a wide range of noncanonical interactions that are not present in DNA. Among them, the recently classified base phosphate (BPh) interactions belong to the most important ones. Twelve percent of nucleotides in the ribosomal crystal structures are involved in BPh interactions. Here we provide assessment of the energetics of BPh interactions using MP2 computations extrapolated to the complete basis set of atomic orbitals and corrected for higher-order electron correlation effects. (en)
Title	Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations (en)
skos:prefLabel	Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations (en)
skos:notation	RIV/68081707:_____/11:00370405!RIV12-AV0-68081707
http://linked.open...avai/predkladatel	Biofyzikální ústav AV ČR, v.v.i.
http://linked.open...avai/riv/aktivita	P S Z
http://linked.open...avai/riv/aktivity	P(ED1.1.00/02.0068), P(ED2.1.00/03.0058), P(EE2.3.20.0017), P(GA203/09/1476), P(GAP208/10/1742), P(GAP208/10/2302), P(GAP208/11/1822), P(GD203/09/H046), P(GPP301/11/P558), P(IAA400040802), P(LC06030), S, Z(AV0Z50040507), Z(AV0Z50040702)
http://linked.open...iv/cisloPeriodika	41
http://linked.open...vai/riv/dodaniDat	2012
http://linked.open...aciTvurceVysledku	Šponer, Jiří Šponer, Judit E.
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	216175
http://linked.open...ai/riv/idVysledku	RIV/68081707:_____/11:00370405
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	density-functional theory; large ribosomal-subunit; gaussian-basis sets (en)
http://linked.open.../riv/klicoveSlovo	gaussian-basis sets density-functional theory large ribosomal-subunit
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[3DC98E5221E4]
http://linked.open...i/riv/nazevZdroje	Journal of Physical Chemistry A
http://linked.open...in/vavai/riv/obor	BO
http://linked.open...ichTvurcuVysledku	2 (xsd:int)
http://linked.open...cetTvurcuVysledku	8 (xsd:int)
http://linked.open...vavai/riv/projekt	Molecules on the Surfaces of Carbon Nanostructures Central european institute of technology Regional Centre of Advanced Technologies and Materials Teoretické a experimentální studie v prebiotické chemii nukleových kyselin Biomolecular centre Research team development of the Regional Centre of Advanced Technologies and Materials 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 Structure and dynamics of DNA. Advanced computational studies. Mechanism of catalytical self-cleavage of two non-coding RNAs of human patogens
http://linked.open...UplatneniVysledku	2011
http://linked.open...v/svazekPeriodika	115
http://linked.open...iv/tvurceVysledku	Šponer, Jiří Šponer, Judit E. Otyepka, M. Banáš, P. Jurečka, P. Leontis, N. B. Zgarbová, M. Zirbel, C. L.
http://linked.open...ain/vavai/riv/wos	000295700600019
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
issn	1089-5639
number of pages	16 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/jp204820b
is http://linked.open...avai/riv/vysledek of	Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations

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