About: Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

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About: Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters 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)

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://pubs.acs.org/doi/abs/10.1021/ct400154j
Description	We present a refinement of the backbone torsion parameters epsilon and zeta of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as epsilon zeta(OL1), were derived from quantum-mechanical calculations with inclusion of conformation-dependent solvation effects according to the recently reported methodology (J. Chem. Theory Comput. 2012, 7 (9), 2886-2902). The performance of the refined parameters was analyzed by means of extended molecular dynamics (MD) simulations for several representative systems. The results showed that the epsilon zeta(OL1) refinement improves the backbone description of B-DNA double helices and the G-DNA stem. In B-DNA simulations, we observed an average increase of the helical twist and narrowing of the major groove, thus achieving better agreement with X-ray and solution NMR data. We present a refinement of the backbone torsion parameters epsilon and zeta of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as epsilon zeta(OL1), were derived from quantum-mechanical calculations with inclusion of conformation-dependent solvation effects according to the recently reported methodology (J. Chem. Theory Comput. 2012, 7 (9), 2886-2902). The performance of the refined parameters was analyzed by means of extended molecular dynamics (MD) simulations for several representative systems. The results showed that the epsilon zeta(OL1) refinement improves the backbone description of B-DNA double helices and the G-DNA stem. In B-DNA simulations, we observed an average increase of the helical twist and narrowing of the major groove, thus achieving better agreement with X-ray and solution NMR data. (en)
Title	Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters (en)
skos:prefLabel	Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters (en)
skos:notation	RIV/00216224:14740/13:00069532!RIV14-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(GAP208/10/1742)
http://linked.open...iv/cisloPeriodika	5
http://linked.open...vai/riv/dodaniDat	2014
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	Masarykova univerzita / Středoevropský technologický institut
http://linked.open...dnocenehoVysledku	111329
http://linked.open...ai/riv/idVysledku	RIV/00216224:14740/13:00069532
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	MOLECULAR-DYNAMICS SIMULATIONS; PHOSPHORUS CHEMICAL-SHIFTS; SUGAR-PHOSPHATE BACKBONE; NUCLEIC-ACID STRUCTURES; BASIS-SET CONVERGENCE; B-II TRANSITIONS; CRYSTAL-STRUCTURES; A-TRACT; CONFORMATIONAL PROPERTIES; RELATIVE FLEXIBILITY (en)
http://linked.open.../riv/klicoveSlovo	NUCLEIC-ACID STRUCTURES SUGAR-PHOSPHATE BACKBONE A-TRACT B-II TRANSITIONS BASIS-SET CONVERGENCE CONFORMATIONAL PROPERTIES PHOSPHORUS CHEMICAL-SHIFTS RELATIVE FLEXIBILITY CRYSTAL-STRUCTURES MOLECULAR-DYNAMICS SIMULATIONS
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[04B1EB1161A0]
http://linked.open...i/riv/nazevZdroje	Journal of Chemical Theory and Computation
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	6 (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 Research team development of the Regional Centre of Advanced Technologies and Materials
http://linked.open...UplatneniVysledku	2013
http://linked.open...v/svazekPeriodika	9
http://linked.open...iv/tvurceVysledku	Otyepka, Michal Šponer, Jiří Jurečka, Petr Cheatham, Thomas E III Luque, Javier F. Zgarbova, Marie
http://linked.open...ain/vavai/riv/wos	000319184800020
issn	1549-9618
number of pages	16 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/ct400154j
http://localhost/t...ganizacniJednotka	14740

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