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Statements

Subject Item
n2:RIV%2F00216224%3A14740%2F13%3A00069532%21RIV14-MSM-14740___
rdf:type
n12:Vysledek skos:Concept
rdfs:seeAlso
http://pubs.acs.org/doi/abs/10.1021/ct400154j
dcterms: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.
dcterms: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
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
skos:notation
RIV/00216224:14740/13:00069532!RIV14-MSM-14740___
n12:predkladatel
n18:orjk%3A14740
n3:aktivita
n6:P n6:I
n3:aktivity
I, P(ED1.1.00/02.0068), P(ED2.1.00/03.0058), P(EE2.3.20.0017), P(GAP208/10/1742)
n3:cisloPeriodika
5
n3:dodaniDat
n9:2014
n3:domaciTvurceVysledku
n20:3223779
n3:druhVysledku
n21:J
n3:duvernostUdaju
n19:S
n3:entitaPredkladatele
n8:predkladatel
n3:idSjednocenehoVysledku
111329
n3:idVysledku
RIV/00216224:14740/13:00069532
n3:jazykVysledku
n13:eng
n3: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
n3:klicoveSlovo
n5:NUCLEIC-ACID%20STRUCTURES n5:MOLECULAR-DYNAMICS%20SIMULATIONS n5:A-TRACT n5:PHOSPHORUS%20CHEMICAL-SHIFTS n5:RELATIVE%20FLEXIBILITY n5:SUGAR-PHOSPHATE%20BACKBONE n5:CONFORMATIONAL%20PROPERTIES n5:CRYSTAL-STRUCTURES n5:B-II%20TRANSITIONS n5:BASIS-SET%20CONVERGENCE
n3:kodStatuVydavatele
US - Spojené státy americké
n3:kontrolniKodProRIV
[04B1EB1161A0]
n3:nazevZdroje
Journal of Chemical Theory and Computation
n3:obor
n10:CF
n3:pocetDomacichTvurcuVysledku
1
n3:pocetTvurcuVysledku
6
n3:projekt
n7:ED2.1.00%2F03.0058 n7:ED1.1.00%2F02.0068 n7:EE2.3.20.0017 n7:GAP208%2F10%2F1742
n3:rokUplatneniVysledku
n9:2013
n3:svazekPeriodika
9
n3:tvurceVysledku
Jurečka, Petr Otyepka, Michal Cheatham, Thomas E III Luque, Javier F. Šponer, Jiří Zgarbova, Marie
n3:wos
000319184800020
s:issn
1549-9618
s:numberOfPages
16
n14:doi
10.1021/ct400154j
n11:organizacniJednotka
14740