About: Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

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About: Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome 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
rdfs:seeAlso	http://pubs.acs.org/doi/abs/10.1021/jz500557y
Description	We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation. We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation. (en)
Title	Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome (en)
skos:prefLabel	Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome (en)
skos:notation	RIV/00216224:14740/14:00076672!RIV15-MSM-14740___
http://linked.open...avai/riv/aktivita	I P
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)
http://linked.open...iv/cisloPeriodika	10
http://linked.open...vai/riv/dodaniDat	2015
http://linked.open...aciTvurceVysledku	Havrila, Marek 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	30283
http://linked.open...ai/riv/idVysledku	RIV/00216224:14740/14:00076672
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	DELTA-VIRUS RIBOZYME; AMBER FORCE-FIELD; REPLICA-EXCHANGE METHOD; SAM-II RIBOSWITCH; RNA KISSING-LOOP; STRUCTURAL DYNAMICS; QUADRUPLEX DNA; EXPLICIT SOLVENT; ENERGY LANDSCAPES; BINDING-SITES (en)
http://linked.open.../riv/klicoveSlovo	ENERGY LANDSCAPES EXPLICIT SOLVENT QUADRUPLEX DNA REPLICA-EXCHANGE METHOD RNA KISSING-LOOP SAM-II RIBOSWITCH BINDING-SITES STRUCTURAL DYNAMICS AMBER FORCE-FIELD DELTA-VIRUS RIBOZYME
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[78B92F707B0D]
http://linked.open...i/riv/nazevZdroje	The Journal of Physical Chemistry Letters
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	2 (xsd:int)
http://linked.open...cetTvurcuVysledku	9 (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
http://linked.open...UplatneniVysledku	2014
http://linked.open...v/svazekPeriodika	5
http://linked.open...iv/tvurceVysledku	Otyepka, Michal Šponer, Jiří Banáš, Pavel Jurečka, Petr Zgarbová, Marie Kührová, Petra Krepl, Miroslav Stadlbauer, Petr Havrila, Marek
http://linked.open...ain/vavai/riv/wos	000336199000027
issn	1948-7185
number of pages	12 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/jz500557y
http://localhost/t...ganizacniJednotka	14740

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