Zobrazeno 1 - 10
of 39
pro vyhledávání: '"Marie Zgarbová"'
Autor:
Marie Zgarbová
Publikováno v:
Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis, Vol 60, Iss 8, Pp 299-306 (2012)
The current scientific methods describing gardens and landscapes all over the world are not always sufficient for the purpose of deep understanding of specific and close relations between landscape/garden and its inhabitants/visitors. A new dimension
Externí odkaz:
https://doaj.org/article/38475f19cf42448c8c6adc658005b3e5
Publikováno v:
Journal of Chemical Theory and Computation. 18:6989-6999
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::81f2c013f8eec667e13e3d7b1eb883da
https://doi.org/10.1021/acs.jctc.2c00733
https://doi.org/10.1021/acs.jctc.2c00733
Autor:
Jakub Šebera, Marie Zgarbová, Ondřej Páv, Vladimír Sychrovský, Jiří Fukal, Miloš Buděšínský, Petr Jurečka
Publikováno v:
Journal of Computational Chemistry. 43:132-143
A method for averaging of NMR parameters by molecular dynamics (MD) has been derived from the method of statistical averaging in MD snapshots, benchmarked and applied to structurally dynamic interpretation of the 31 P NMR shift (δ31P ) in DNA phosph
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::da180054fb432e67c7855487091c407f
https://doi.org/10.1002/jcc.26778
https://doi.org/10.1002/jcc.26778
Autor:
Modesto Orozco, Pavel Banáš, Daniel Hollas, Marie Zgarbová, Petr Jurečka, Jiří Šponer, Thomas E. Cheatham, Michal Otyepka
Publikováno v:
J Chem Theory Comput
The RNA hairpin loops represent important RNA topologies with indispensable biological functions in RNA folding and tertiary interactions. 5′-UNCG-3′ and 5′-GNRA-3′ RNA tetraloops are the most important classes of RNA hairpin loops. Both tetr
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::234f55914b641dec0b20edd620f584b0
https://pubmed.ncbi.nlm.nih.gov/35283696
https://pubmed.ncbi.nlm.nih.gov/35283696
When DNA interacts with a protein, its structure often undergoes significant conformational adaptation. Perhaps the most common is the transition from canonical B-DNA towards the A-DNA form, which is not a two-state, but rather a continuous transitio
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::0452c3fddfa151a376497919631cfb1f
https://doi.org/10.1101/2022.01.13.476176
https://doi.org/10.1101/2022.01.13.476176
Autor:
Jiří, Fukal, Miloš, Buděšínský, Ondřej, Páv, Petr, Jurečka, Marie, Zgarbová, Jakub, Šebera, Vladimír, Sychrovský
Publikováno v:
Journal of computational chemistryREFERENCES. 43(2)
A method for averaging of NMR parameters by molecular dynamics (MD) has been derived from the method of statistical averaging in MD snapshots, benchmarked and applied to structurally dynamic interpretation of the
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::1ae22b779901dcbbc914fc56907d1003
https://pubmed.ncbi.nlm.nih.gov/34729803
https://pubmed.ncbi.nlm.nih.gov/34729803
Although current AMBER force fields are relatively accurate for canonical B-DNA, many non-canonical structures are still described incorrectly. As non-canonical motifs are attracting increasing attention due to the role they play in living organisms,
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b4ca4dfc9e63aeeaef39e06cb5c0cc01
https://doi.org/10.1101/2021.07.11.451955
https://doi.org/10.1101/2021.07.11.451955
Publikováno v:
Journal of Chemical Theory and Computation. 14:319-328
The A/B transition is a basic element of DNA conformational change. Because of its involvement in the sensing of the ionic conditions by DNA and in specific protein-DNA interactions, this transition is important for biological functions of DNA. There
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::907d2afe4a0ac826fdad11e81c6a0d4f
https://doi.org/10.1021/acs.jctc.7b00926
https://doi.org/10.1021/acs.jctc.7b00926
Publikováno v:
The Journal of Physical Chemistry B. 121:2420-2433
The sugar–phosphate backbone of RNA can exist in diverse rotameric substates, giving RNA molecules enormous conformational variability. The most frequent noncanonical backbone conformation in RNA is α/γ = t/t, which is derived from the canonical
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c9b1f19489091804d50b6e828afd4a44
https://doi.org/10.1021/acs.jpcb.7b00262
https://doi.org/10.1021/acs.jpcb.7b00262
Autor:
Vojtěch Mlýnský, Pavel Banáš, Petra Kührová, Marie Zgarbová, Michal Otyepka, Miroslav Krepl, Jiří Šponer, Robert B. Best, Giovanni Bussi
Publikováno v:
J Chem Theory Comput
Molecular dynamics (MD) simulations became a leading tool for investigation of structural dynamics of nucleic acids. Despite recent efforts to improve the empirical potentials (force fields, ffs), RNA ffs have persisting deficiencies, which hamper th
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::860cb8c0b161c9757640a32e049572f0
https://doi.org/10.1021/acs.jctc.9b01189
https://doi.org/10.1021/acs.jctc.9b01189