Reference Simulations of Noncanonical Nucleic Acids with Different chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F12%3A33142859" target="_blank" >RIV/61989592:15310/12:33142859 - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/12:00379846 RIV/00216224:14740/12:00057523
Result on the web
<a href="http://dx.doi.org/10.1021/ct300275s" target="_blank" >http://dx.doi.org/10.1021/ct300275s</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/ct300275s" target="_blank" >10.1021/ct300275s</a>

Result language
angličtina
Original language name
Reference Simulations of Noncanonical Nucleic Acids with Different chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA
Original language description
Refinement of empirical force fields for nucleic acids requires their extensive testing using as wide range of systems as possible. However, finding unambiguous reference data is not easy. In this paper, we analyze four systems that we suggest should beincluded in standard portfolio of molecules to test nucleic acids force fields, namely, parallel and antiparallel stranded DNA guanine quadruplex stems, RNA quadruplex stem, and Z-DNA. We highlight parameters that should be monitored to assess the forcefield performance. The work is primarily based on 8.4 mu s of 100-250 ns trajectories analyzed in detail followed by 9.6 mu s of additional selected backup trajectories that were monitored to verify that the results of the initial analyses are correct. Four versions of the Cornell et al. AMBER force field are tested, including an entirely new parm chi(OL4) variant with chi dihedral specifically reparametrized for DNA molecules containing synnucleotides. We test also different water model
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
2012
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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