About: The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies

Facets (new session)
Description
Metadata
Settings
- owl:sameAs
- Inference Rule:

About: The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies Goto Sponge NotDistinct Permalink

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

Attributes	Values
rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	Knowledge of geometrical and physico-chemical properties of the sugar-phosphate backbone substantially contributes to the comprehension of the structural dynamics, function and evolution of nucleic acids. We provide a side by side overview of structural biology/bioinformatics, quantum chemical and molecular mechanical/simulation studies of the nucleic acids backbone. We highlight main features, advantages and limitations of these techniques, with a special emphasis given to their synergy. The present status of the research is then illustrated by selected examples which include classification of DNA and RNA backbone families, benchmark structure-energy quantum chemical calculations, parameterization of the dihedral space of simulation force fields, incorporation of arsenate into DNA, sugar-phosphate backbone selfcleavage in small RNA enzymes, and intricate geometries of the backbone in recurrent RNA building blocks. Although not apparent from the current literature showing limited overlaps between the QM, simulation and bioinformatics studies of the nucleic acids backbone, there in fact should be a major cooperative interaction between these three approaches in studies of the sugar-phosphate backbone. Knowledge of geometrical and physico-chemical properties of the sugar-phosphate backbone substantially contributes to the comprehension of the structural dynamics, function and evolution of nucleic acids. We provide a side by side overview of structural biology/bioinformatics, quantum chemical and molecular mechanical/simulation studies of the nucleic acids backbone. We highlight main features, advantages and limitations of these techniques, with a special emphasis given to their synergy. The present status of the research is then illustrated by selected examples which include classification of DNA and RNA backbone families, benchmark structure-energy quantum chemical calculations, parameterization of the dihedral space of simulation force fields, incorporation of arsenate into DNA, sugar-phosphate backbone selfcleavage in small RNA enzymes, and intricate geometries of the backbone in recurrent RNA building blocks. Although not apparent from the current literature showing limited overlaps between the QM, simulation and bioinformatics studies of the nucleic acids backbone, there in fact should be a major cooperative interaction between these three approaches in studies of the sugar-phosphate backbone. (en)
Title	The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies (en)
skos:prefLabel	The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies (en)
skos:notation	RIV/61989592:15310/12:33142854!RIV13-MSM-15310___
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(ED1.1.00/02.0068), P(ED2.1.00/03.0058), P(GA203/09/1476), P(GAP208/10/2302), P(GAP208/11/1822), P(GAP208/12/1878), P(GBP305/12/G034), P(GD203/09/H046), Z(AV0Z50040702), Z(MSM6046137302)
http://linked.open...iv/cisloPeriodika	44
http://linked.open...vai/riv/dodaniDat	2013
http://linked.open...aciTvurceVysledku	Otyepka, Michal Banáš, Pavel Jurečka, Petr Zgarbová, Marie
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	Univerzita Palackého v Olomouci / Přírodovědecká fakulta
http://linked.open...dnocenehoVysledku	131752
http://linked.open...ai/riv/idVysledku	RIV/61989592:15310/12:33142854
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	self-cleaving ribozymes; main-group thermochemistry; intrinsic conformational properties; single-strand breaks; intramolecular hydrogen-bonds; density-functional calculations; nucleic-acid backbone; molecular-dynamics simulations; hepatitis-delta-virus (en)
http://linked.open.../riv/klicoveSlovo	single-strand breaks main-group thermochemistry hepatitis-delta-virus intramolecular hydrogen-bonds intrinsic conformational properties nucleic-acid backbone self-cleaving ribozymes molecular-dynamics simulations density-functional calculations
http://linked.open...odStatuVydavatele	GB - Spojené království Velké Británie a Severního Irska
http://linked.open...ontrolniKodProRIV	[251CA4469AAF]
http://linked.open...i/riv/nazevZdroje	Physical Chemistry Chemical Physics
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	4 (xsd:int)
http://linked.open...cetTvurcuVysledku	8 (xsd:int)
http://linked.open...vavai/riv/projekt	Catalytic strategies of RNA and RNP enzymes studied by multi-scale computational approach Centre for RNA Biology Central european institute of technology Regional Centre of Advanced Technologies and Materials Teoretické a experimentální studie v prebiotické chemii nukleových kyselin Structural dynamics, molecular interactions and function of key RNA motifs Biochemistry on the crossroad from in silico to in vitro Structure and dynamics of DNA. Advanced computational studies.
http://linked.open...UplatneniVysledku	2012
http://linked.open...v/svazekPeriodika	14
http://linked.open...iv/tvurceVysledku	Otyepka, Michal Šponer, Jiří Svozil, Daniel Mládek, Arnošt Banáš, Pavel Jurečka, Petr Zgarbová, Marie Šponerová, Judit E.
http://linked.open...ain/vavai/riv/wos	000310153300002
http://linked.open...n/vavai/riv/zamer	Genome and epigenome: 1D and 3D Structure, Dynamics, Interactions with Proteins and Functions Preparation and research of functional materials and material technologies using micro- and nanoscopic methods
issn	1463-9076
number of pages	21 (xsd:int)
http://bibframe.org/vocab/doi	10.1039/c2cp41987d
http://localhost/t...ganizacniJednotka	15310

Faceted Search & Find service v1.16.118 as of Jun 21 2024

Alternative Linked Data Documents: ODE Content Formats:

RDF

ODATA

Microdata

About

OpenLink Virtuoso version 07.20.3240 as of Jun 21 2024, on Linux (x86_64-pc-linux-gnu), Single-Server Edition (126 GB total memory, 35 GB memory in use)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2024 OpenLink Software