Rezultati - Pavel Banáš

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  1. 1
    Free Energy Landscape of GAGA and UUCG RNA Tetraloops

    Free Energy Landscape of GAGA and UUCG RNA Tetraloops od Sandro Bottaro, Pavel Banáš, Jiřı́ Šponer, Giovanni Bussi

    Izdano 2016
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  2. 2
    Protonation States of the Key Active Site Residues and Structural Dynamics of the <i>glmS</i> Riboswitch As Revealed by Molecular Dynamics

    Protonation States of the Key Active Site Residues and Structural Dynamics of the <i>glmS</i> Riboswitch As Revealed by Molecular Dynamics od Pavel Banáš, Nils G. Walter, Jiřı́ Šponer, Michal Otyepka

    Izdano 2010
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  3. 3
    Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes

    Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes od Petra Kührová, Vojtěch Mlýnský, Michal Otyepka, Jiřı́ Šponer, Pavel Banáš

    Izdano 2023
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  4. 4
    Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM

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

    Izdano 2009
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  5. 5
    CAVER: a new tool to explore routes from protein clefts, pockets and cavities

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

    Izdano 2006
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  6. 6
    Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes

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

    Izdano 2019
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  7. 7
    Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides

    Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides od Vojtěch Mlýnský, Petra Kührová, Tomáš Kühr, Michal Otyepka, Giovanni Bussi, Pavel Banáš, Jiřı́ Šponer

    Izdano 2020
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  8. 8
    Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations

    Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations od Vojtěch Mlýnský, Petra Kührová, Petr Stadlbauer, Miroslav Krepl, Michal Otyepka, Pavel Banáš, Jiřı́ Šponer

    Izdano 2023
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  9. 9
    Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes

    Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes od Barbora Knappeová, Vojtěch Mlýnský, Martin Pykal, Jiřı́ Šponer, Pavel Banáš, Michal Otyepka, Miroslav Krepl

    Izdano 2024
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  10. 10
    Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H<sup>+</sup> Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme

    Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H<sup>+</sup> Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme od Vojtěch Mlýnský, Pavel Banáš, Daniel Hollas, Kamila Réblová, Nils G. Walter, Jiřı́ Šponer, Michal Otyepka

    Izdano 2010
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  11. 11
    Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

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

    Izdano 2011
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  12. 12
    Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies

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

    Izdano 2016
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  13. 13
    Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations

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

    Izdano 2015
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  14. 14
    Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field

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

    Izdano 2022
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  15. 15
    Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of the UUCG RNA Tetraloop and Other Systems

    Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of the UUCG RNA Tetraloop and Other Systems od Vojtěch Mlýnský, Petra Kührová, Martin Pykal, Miroslav Krepl, Petr Stadlbauer, Michal Otyepka, Pavel Banáš, Jiřı́ Šponer

    Izdano 2025
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  16. 16
    Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

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

    Izdano 2010
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  17. 17
    Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

    Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome od Jiřı́ Šponer, Pavel Banáš, Petr Jurečka, Marie Zgarbová, Petra Kührová, Marek Havrila, Miroslav Krepl, Petr Stadlbauer, Michal Otyepka

    Izdano 2014
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  18. 18
    Anatomy of enzyme channels

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

    Izdano 2014
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  19. 19
    Folding of guanine quadruplex molecules–funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies

    Folding of guanine quadruplex molecules–funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies od Jiřı́ Šponer, Giovanni Bussi, Petr Stadlbauer, Petra Kührová, Pavel Banáš, Barira Islam, Shozeb Haider, Stephen Neidle, Michal Otyepka

    Izdano 2016
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  20. 20
    Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA

    Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA od Miroslav Krepl, Marie Zgarbová, Petr Stadlbauer, Michal Otyepka, Pavel Banáš, Jaroslav Koča, Thomas E. Cheatham, Petr Jurečka, Jiřı́ Šponer

    Izdano 2012
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