Search Results - "Zgarbova, M"

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles by Zgarbová, Marie, Otyepka, Michal, Šponer, Jiří, Mládek, Arnošt, Banáš, Pavel, Cheatham, Thomas E, Jurečka, Petr

“…We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force field for RNA, χOL. The parameters remove destabilization of the…”
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Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters by Zgarbová, Marie, Luque, F. Javier, Šponer, Jiří, Cheatham, Thomas E, Otyepka, Michal, Jurečka, Petr

“…We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as…”
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Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning by Drsata, Tomas, Spackova, Naa, Jurecka, Petr, Zgarbova, Marie, Sponer, Jiri, Lankas, Filip

“…A-tracts are functionally important DNA sequences which induce helix bending and have peculiar structural properties. While A-tract structure has been…”
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Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics by Banáš, Pavel, Mládek, Arnošt, Otyepka, Michal, Zgarbová, Marie, Jurečka, Petr, Svozil, Daniel, Lankaš, Filip, Šponer, Jiří

“…Sequence-dependent local variations of helical parameters, structure, and flexibility are crucial for molecular recognition processes involving B-DNA…”
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Reference Simulations of Noncanonical Nucleic Acids with Different x Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA by Krepl, M, Zgarbova, M, Stadlbauer, P, Otyepka, M, Banas, P, Koca, J, Cheatham, TE III, Jurecka, P, Sponer, J

“…Refinement of empirical force fields for nucleic acids requires their extensive testing using as wide range of systems as possible. However, finding…”
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Fundamental phenomenological categories of garden and landscape by Zgarbová, Marie

“…The current scientific methods describing gardens and landscapes all over the world are not always sufficient for the purpose of deep understanding of specific…”
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