. "0"^^ . . "DNA structure and function molecular dynamics quantum chemistry base pairs"@en . "Structure and dynamics of DNA. Advanced computational studies."@en . . "26"^^ . . "26"^^ . "2014-03-31+02:00"^^ . . . . . "GAP208/11/1822" . . . "2015-04-23+02:00"^^ . "2015-12-31+01:00"^^ . . "2011-01-01+01:00"^^ . . . "The project will study important features of DNA molecules using state-of-the-art theoretical (computational) approaches: advanced quantum chemical (QM) calculations and explicit solvent molecular dynamics (MD) simulations. The studied issues will include: In-depth QM characterization of the intrinsic stacking signatures of all ten unique B-DNA base pair steps, using conformational scans, experimental geometries and geometries derived by simulations, with the aim to understand relation between base stacking and B-DNA local conformational variations. These computations will be accompanied by microsecond-scale simulations of specific B-DNA oligomers, such as phased A-tracts. Prediction of intermediates in formation/folding of four-stranded DNA molecules (G-DNA and i-DNA) using MD simulations and free energy computations. Complete QM analysis of conformational space of the DNA sugar-phosphate backbone. MD analysis of structural dynamics and sequence-dependence of DNA four-way junctions. Besides substantially improving our basic knowledge about DNA structural dynamics, the project will also contribute to the development of methodology, for example by attempting to refine parameters for description of DNA backbone in the simulation force field."@en . . "Tento projekt bude zam\u011B\u0159en na studium d\u016Fle\u017Eit\u00FDch vlastnost\u00ED molekul DNA, s\u00A0pou\u017Eit\u00EDm nejmodern\u011Bj\u0161\u00EDch teoretick\u00FDch (po\u010D\u00EDta\u010Dov\u00FDch) p\u0159\u00EDstup\u016F: pokro\u010Dil\u00FDch kvantov\u011B chemick\u00FDch (QM) v\u00FDpo\u010Dt\u016F a simulac\u00ED molekulov\u00E9 dynamiky (MD) v\u00A0explicitn\u00EDm solventu. Studovan\u00E1 problematika bude zahrnovat: detailn\u00ED QM charakterizaci signatur stacking interakc\u00ED v\u0161ech deseti jedine\u010Dn\u00FDch dvojic p\u00E1r\u016F b\u00E1z\u00ED B-DNA, s\u00A0pou\u017Eit\u00EDm konforma\u010Dn\u00EDho prohled\u00E1v\u00E1n\u00ED, experiment\u00E1ln\u00EDch geometri\u00ED a geometri\u00ED z\u00EDskan\u00FDch se simulac\u00ED, s\u00A0c\u00EDlem porozum\u011Bt vztahu mezi\u00A0 stackingem b\u00E1z\u00ED a lok\u00E1ln\u00EDmi konforma\u010Dn\u00EDmi variacemi v\u00A0B-DNA. Tyto v\u00FDpo\u010Dty budou dopln\u011Bny mikrosekundov\u00FDmi simulacemi specifick\u00FDch oligomer\u016F B-DNA, jako jsou A-trakty. Projekt se d\u00E1le bude zab\u00FDvat predikc\u00ED intermedi\u00E1t\u016F p\u0159i formov\u00E1n\u00ED \u010Dty\u0159\u0159et\u011Bzcov\u00FDch molekul DNA (G-DNA a i-DNA) s\u00A0pou\u017Eit\u00EDm simulac\u00ED MD a v\u00FDpo\u010Dt\u016F voln\u00E9 energie; kompletn\u00ED QM anal\u00FDzou konforma\u010Dn\u00EDho prostoru cukr-fosf\u00E1tov\u00E9 p\u00E1te\u0159e\u00A0 DNA; MD anal\u00FDzou strukturn\u00ED dynamiky a sekven\u010Dn\u00ED z\u00E1vislosti four-way junctions DNA. Krom\u011B podstatn\u00E9ho roz\u0161\u00ED\u0159en\u00ED na\u0161ich z\u00E1kladn\u00EDch znalost\u00ED o strukturn\u00ED dynamice DNA bude projekt zahrnovat i v\u00FDvoj metodiky, nap\u0159\u00EDklad vylep\u0161en\u00ED parametr\u016F pro popis p\u00E1te\u0159e DNA v\u00A0empirick\u00FDch silov\u00FDch pol\u00EDch." . . . "1"^^ . . "http://www.isvav.cz/projectDetail.do?rowId=GAP208/11/1822"^^ . . "Struktura a dynamika DNA. Pokro\u010Dil\u00E9 po\u010D\u00EDta\u010Dov\u00E9 studie." . "0"^^ . .