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Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids
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SYSNO ASEP 0310366 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids Title Geometrická a elektronická strukturní variabilita cukr-fosfátové páteře v nukleových kyselinách Author(s) Svozil, Daniel (UOCHB-X)
Šponer, Judit E. (BFU-R) RID, ORCID
Marchan, I. (ES)
Pérez, A. (ES)
Cheatham III., T.E. (US)
Forti, F. (ES)
Luque, F.J. (ES)
Orözcö, M. (ES)
Šponer, Jiří (BFU-R) RID, ORCIDSource Title Journal of Physical Chemistry B. - : American Chemical Society - ISSN 1520-6106
Roč. 112, č. 27 (2008), s. 8188-8197Number of pages 10 s. Language eng - English Country US - United States Keywords molecular dynamics ; force field ; quantum chemistry Subject RIV BO - Biophysics R&D Projects LC512 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) IAA400550701 GA AV ČR - Academy of Sciences of the Czech Republic (AV ČR) 1QS500040581 GA AV ČR - Academy of Sciences of the Czech Republic (AV ČR) CEZ AV0Z50040507 - BFU-R (2005-2011) AV0Z50040702 - BFU-R (2007-2013) AV0Z40550506 - UOCHB-X (2005-2011) UT WOS 000257335200031 DOI 10.1021/jp801245h Annotation Quantum chemistry was used to describe alpha/gamma energetics and to access Amber force field parm99 and parmbsc0. This was tested on two models systems: SPM consisting of a sugar and methyl group linked through a phosphodiester bond and sPSOM consisting of two deoxyribose residues (without the bases) connected via a phosphodiester bond. A comparison of the ab initio data with the ff99 potential energy surface clearly reveals an incorrect ff99 force-field description in the regions where the gamma torsion is in the trans conformation. Workplace Institute of Biophysics Contact Jana Poláková, polakova@ibp.cz, Tel.: 541 517 244 Year of Publishing 2009
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