Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions
Kührová, Petra, Mlýnský, Vojtěch, Zgarbová, Marie, Krepl, Miroslav, Bussi, Giovanni, Best, Robert B, Otyepka, Michal, Šponer, Jiří, Banáš, Pavel
Published in Journal of chemical theory and computation (14.05.2019)
Published in Journal of chemical theory and computation (14.05.2019)
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Journal Article
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
Zgarbová, Marie, Otyepka, Michal, Šponer, Jiří, Mládek, Arnošt, Banáš, Pavel, Cheatham, Thomas E, Jurečka, Petr
Published in Journal of chemical theory and computation (13.09.2011)
Published in Journal of chemical theory and computation (13.09.2011)
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Journal Article
Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters
Zgarbová, Marie, Luque, F. Javier, Šponer, Jiří, Cheatham, Thomas E, Otyepka, Michal, Jurečka, Petr
Published in Journal of chemical theory and computation (14.05.2013)
Published in Journal of chemical theory and computation (14.05.2013)
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Journal Article
Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins
Banáš, Pavel, Hollas, Daniel, Zgarbová, Marie, Jurečka, Petr, Orozco, Modesto, Cheatham, Thomas E, Šponer, Jiří, Otyepka, Michal
Published in Journal of chemical theory and computation (14.12.2010)
Published in Journal of chemical theory and computation (14.12.2010)
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Journal Article
Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome
Šponer, Jiří, Banáš, Pavel, Jurečka, Petr, Zgarbová, Marie, Kührová, Petra, Havrila, Marek, Krepl, Miroslav, Stadlbauer, Petr, Otyepka, Michal
Published in The journal of physical chemistry letters (15.05.2014)
Published in The journal of physical chemistry letters (15.05.2014)
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Journal Article
The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies
SPONER, Jiří, MLADEK, Arnost, SPONER, Judit E, SVOZIL, Daniel, ZGARBOVA, Marie, BANAS, Pavel, JURECKA, Petr, OTYEPKA, Michal
Published in Physical chemistry chemical physics : PCCP (28.11.2012)
Published in Physical chemistry chemical physics : PCCP (28.11.2012)
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Journal Article
Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics
Banáš, Pavel, Mládek, Arnošt, Otyepka, Michal, Zgarbová, Marie, Jurečka, Petr, Svozil, Daniel, Lankaš, Filip, Šponer, Jiří
Published in Journal of chemical theory and computation (10.07.2012)
Published in Journal of chemical theory and computation (10.07.2012)
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Journal Article
Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base–Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations
Zgarbová, Marie, Jurečka, Petr, Banáš, Pavel, Otyepka, Michal, Šponer, Judit E, Leontis, Neocles B, Zirbel, Craig L, Šponer, Jiří
Published in The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory (20.10.2011)
Published in The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory (20.10.2011)
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Journal Article
Assessing the Current State of Amber Force Field Modifications for DNA
Galindo-Murillo, Rodrigo, Robertson, James C, Zgarbová, Marie, Šponer, Jiří, Otyepka, Michal, Jurečka, Petr, Cheatham, Thomas E
Published in Journal of chemical theory and computation (09.08.2016)
Published in Journal of chemical theory and computation (09.08.2016)
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Journal Article
Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B‑DNA
Zgarbová, Marie, Šponer, Jiří, Otyepka, Michal, Cheatham, Thomas E., Galindo-Murillo, Rodrigo, Jurečka, Petr
Published in Journal of chemical theory and computation (08.12.2015)
Published in Journal of chemical theory and computation (08.12.2015)
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Journal Article
Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA
Zgarbová, Marie, Otyepka, Michal, Šponer, Jiří, Lankaš, Filip, Jurečka, Petr
Published in Journal of chemical theory and computation (12.08.2014)
Published in Journal of chemical theory and computation (12.08.2014)
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Journal Article
A- to B‑DNA Transition in AMBER Force Fields and Its Coupling to Sugar Pucker
Zgarbová, Marie, Jurečka, Petr, Šponer, Jiří, Otyepka, Michal
Published in Journal of chemical theory and computation (09.01.2018)
Published in Journal of chemical theory and computation (09.01.2018)
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Journal Article
Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA
Krepl, Miroslav, Zgarbová, Marie, Stadlbauer, Petr, Otyepka, Michal, Banáš, Pavel, Koča, Jaroslav, Cheatham, Thomas E, Jurečka, Petr, Šponer, Jiří
Published in Journal of chemical theory and computation (10.07.2012)
Published in Journal of chemical theory and computation (10.07.2012)
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Journal Article
Noncanonical α/γ Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field
Zgarbová, Marie, Jurečka, Petr, Banáš, Pavel, Havrila, Marek, Šponer, Jiří, Otyepka, Michal
Published in The journal of physical chemistry. B (23.03.2017)
Published in The journal of physical chemistry. B (23.03.2017)
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Journal Article
Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences
Zgarbová, Marie, Jurečka, Petr, Lankaš, Filip, Cheatham, Thomas E, Šponer, Jiří, Otyepka, Michal
Published in Journal of chemical information and modeling (27.02.2017)
Published in Journal of chemical information and modeling (27.02.2017)
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Journal Article
Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with ε/ζ Force Field Reparametrizations
Mlýnský, Vojtěch, Kührová, Petra, Zgarbová, Marie, Jurečka, Petr, Walter, Nils G, Otyepka, Michal, Šponer, Jiří, Banáš, Pavel
Published in The journal of physical chemistry. B (19.03.2015)
Published in The journal of physical chemistry. B (19.03.2015)
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Journal Article