检索结果 - Banáš, Pavel

Protonation states of the key active site residues and structural dynamics of glmS riboswitch as reveled by molecular dynamics 由 Banáš, Pavel, Walter, Nils G., Šponer, Jiří, Otyepka, Michal

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Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM 由 Banáš, Pavel, Jurečka, Petr, Walter, Nils G., Šponer, Jiří, Otyepka, Michal

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QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms 由 Mlýnský, Vojtěch, Banáš, Pavel, Walter, Nils G., Šponer, Jiří, Otyepka, Michal

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Molecular Mechanism of preQ(1) Riboswitch Action: A Molecular Dynamics Study 由 Banáš, Pavel, Sklenovský, Petr, Wedekind, Joseph E., Šponer, Jiří, Otyepka, Michal

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The Role of an Active Site Mg(2+) in HDV Ribozyme Self-Cleavage: Insights from QM/MM Calculations 由 Mlýnský, Vojtěch, Walter, Nils G., Šponer, Jiří, Otyepka, Michal, Banáš, Pavel

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Chemical Feasibility of the General Acid/Base Mechanism of glmS Ribozyme Self-Cleavage 由 Dubecký, Matúš, Walter, Nils G., Šponer, Jiří, Otyepka, Michal, Banáš, Pavel

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CAVER: a new tool to explore routes from protein clefts, pockets and cavities 由 Petřek, Martin, Otyepka, Michal, Banáš, Pavel, Košinová, Pavlína, Koča, Jaroslav, Damborský, Jiří

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Wobble Pairs of the HDV Ribozyme Play Specific Roles in Stabilization of Active Site Dynamics 由 Sripathi, Kamali N., Banáš, Pavel, Reblova, Kamila, Šponer, Jiři, Otyepka, Michal, Walter, Nils G.

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Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes 由 Stadlbauer, Petr, Kührová, Petra, Vicherek, Lukáš, Banáš, Pavel, Otyepka, Michal, Trantírek, Lukáš, Šponer, Jiří

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General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility 由 Banáš, Pavel, Rulíšek, Lubomír, Hánošová, Veronika, Svozil, Daniel, Walter, Nils G., Šponer, Jiří, Otyepka, Michal

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Extensive Molecular Dynamics Simulations Show That Canonical G8 and Protonated A38H(+) Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme 由 Mlýnský, Vojtěch, Banáš, Pavel, Hollas, Daniel, Réblová, Kamila, Walter, Nils G., Šponer, Jiří, Otyepka, Michal

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

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Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape 由 Sripathi, Kamali N., Tay, Wendy W., Banáš, Pavel, Otyepka, Michal, Šponer, Jiří, Walter, Nils G.

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Structural dynamics of propeller loop: towards folding of RNA G-quadruplex 由 Havrila, Marek, Stadlbauer, Petr, Kührová, Petra, Banáš, Pavel, Mergny, Jean-Louis, Otyepka, Michal, Šponer, Jiří

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Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies 由 Kührová, Petra, Best, Robert B., Bottaro, Sandro, Bussi, Giovanni, Šponer, Jiří, Otyepka, Michal, Banáš, Pavel

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Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations 由 Stadlbauer, Petr, Kührová, Petra, Banáš, Pavel, Koča, Jaroslav, Bussi, Giovanni, Trantírek, Lukáš, Otyepka, Michal, Šponer, Jiří

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Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field 由 Fröhlking, Thorben, Mlýnský, Vojtěch, Janeček, Michal, Kührová, Petra, Krepl, Miroslav, Banáš, Pavel, Šponer, Jiří, Bussi, Giovanni

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Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins 由 Banáš, Pavel, Hollas, Daniel, Zgarbová, Marie, Jurečka, Petr, Orozco, Modesto, Cheatham, Thomas E., Šponer, Jiří, Otyepka, Michal

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Anatomy of enzyme channels 由 Pravda, Lukáš, Berka, Karel, Svobodová Vařeková, Radka, Sehnal, David, Banáš, Pavel, Laskowski, Roman A, Koča, Jaroslav, Otyepka, Michal

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Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA 由 Krepl, Miroslav, Zgarbová, Marie, Stadlbauer, Petr, Otyepka, Michal, Banáš, Pavel, Koča, Jaroslav, Cheatham, Thomas E., Jurečka, Petr, Šponer, Jiří

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