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

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F13%3A33148177" target="_blank" >RIV/61989592:15310/13:33148177 - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/13:00394840 RIV/00216224:14740/13:00069532
Result on the web
<a href="http://pubs.acs.org/doi/abs/10.1021/ct400154j" target="_blank" >http://pubs.acs.org/doi/abs/10.1021/ct400154j</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/ct400154j" target="_blank" >10.1021/ct400154j</a>

Result language
angličtina
Original language name
Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters
Original language 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 ofconformation-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 forseveral 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. The balance between populations of BI and BII backbone substates was shifted toward the BII state, in better agreement with ensemble-refined solutio
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
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Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2013
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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