Search Results - "Kührová, Petra"

Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions by Kührová, Petra, Mlýnský, Vojtěch, Zgarbová, Marie, Krepl, Miroslav, Bussi, Giovanni, Best, Robert B, Otyepka, Michal, Šponer, Jiří, Banáš, Pavel

“…Molecular dynamics (MD) simulations became a leading tool for investigation of structural dynamics of nucleic acids. Despite recent efforts to improve the…”
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Role of Ionizable Lipids in SARS-CoV‑2 Vaccines As Revealed by Molecular Dynamics Simulations: From Membrane Structure to Interaction with mRNA Fragments by Paloncýová, Markéta, Čechová, Petra, Šrejber, Martin, Kührová, Petra, Otyepka, Michal

“…Recent advances in RNA-based medicine have provided new opportunities for the global current challenge, i.e., the COVID-19 pandemic. Novel vaccines are based…”
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Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes by Kührová, Petra, Mlýnský, Vojtěch, Otyepka, Michal, Šponer, Jiří, Banáš, Pavel

“…RNA molecules play a key role in countless biochemical processes. RNA interactions, which are of highly diverse nature, are determined by the fact that RNA is…”
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Atomistic Insights into Organization of RNA-Loaded Lipid Nanoparticles by Paloncýová, Markéta, Šrejber, Martin, Čechová, Petra, Kührová, Petra, Zaoral, Filip, Otyepka, Michal

“…RNA-based therapies have shown promise in a wide range of applications, from cancer therapy, treatment of inherited diseases to vaccination. Encapsulation of…”
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Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies by Kührová, Petra, Best, Robert B, Bottaro, Sandro, Bussi, Giovanni, Šponer, Jiří, Otyepka, Michal, Banáš, Pavel

“…The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are…”
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Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field by Fröhlking, Thorben, Mlýnský, Vojtěch, Janeček, Michal, Kührová, Petra, Krepl, Miroslav, Banáš, Pavel, Šponer, Jiří, Bussi, Giovanni

“…The capability of current force fields to reproduce RNA structural dynamics is limited. Several methods have been developed to take advantage of experimental…”
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W‑RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model by Janeček, Michal, Kührová, Petra, Mlýnský, Vojtěch, Otyepka, Michal, Šponer, Jiří, Banáš, Pavel

“…Representation of electrostatic interactions by a Coulombic pairwise potential between atom-centered partial charges is a fundamental and crucial part of…”
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Correction to “Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes” by Kührová, Petra, Mlýnský, Vojtěch, Otyepka, Michal, Šponer, Jiří, Banáš, Pavel

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

“…We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the…”
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UUCG RNA Tetraloop as a Formidable Force-Field Challenge for MD Simulations by Mráziková, Klaudia, Mlýnský, Vojtěch, Kührová, Petra, Pokorná, Pavlína, Kruse, Holger, Krepl, Miroslav, Otyepka, Michal, Banáš, Pavel, Šponer, Jiří

“…Explicit solvent atomistic molecular dynamics (MD) simulations represent an established technique to study structural dynamics of RNA molecules and an…”
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Computer Aided Development of Nucleic Acid Applications in Nanotechnologies by Paloncýová, Markéta, Pykal, Martin, Kührová, Petra, Banáš, Pavel, Šponer, Jiří, Otyepka, Michal

“…Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology‐related applications is a growing field with broad application potential, ranging…”
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Are Waters around RNA More than Just a Solvent? – An Insight from Molecular Dynamics Simulations by Kührová, Petra, Otyepka, Michal, Šponer, Jiří, Banáš, Pavel

“…Hydrating water molecules are believed to be an inherent part of the RNA structure and have a considerable impact on RNA conformation. However, the magnitude…”
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Structural dynamics of propeller loop: towards folding of RNA G-quadruplex by Havrila, Marek, Stadlbauer, Petr, Kührová, Petra, Banáš, Pavel, Mergny, Jean-Louis, Otyepka, Michal, Šponer, Jiří

“…Abstract We have carried out an extended set of standard and enhanced-sampling MD simulations (for a cumulative simulation time of 620 μs) with the aim to…”
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Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics by Haldar, Susanta, Kührová, Petra, Banáš, Pavel, Spiwok, Vojtěch, Šponer, Jiří, Hobza, Pavel, Otyepka, Michal

“…RNA hairpins capped by 5′-GNRA-3′ or 5′-UNCG-3′ tetraloops (TLs) are prominent RNA structural motifs. Despite their small size, a wealth of experimental data,…”
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Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with ε/ζ Force Field Reparametrizations by Mlýnský, Vojtěch, Kührová, Petra, Zgarbová, Marie, Jurečka, Petr, Walter, Nils G, Otyepka, Michal, Šponer, Jiří, Banáš, Pavel

“…X-ray crystallography can provide important insights into the structure of RNA enzymes (ribozymes). However, the details of a ribozyme’s active site…”
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Atomically resolved imaging of the conformations and adsorption geometries of individual β-cyclodextrins with non-contact AFM by Grabarics, Márkó, Mallada, Benjamín, Edalatmanesh, Shayan, Jiménez-Martín, Alejandro, Pykal, Martin, Ondráček, Martin, Kührová, Petra, Struwe, Weston B., Banáš, Pavel, Rauschenbach, Stephan, Jelínek, Pavel, de la Torre, Bruno

“…Glycans, consisting of covalently linked sugar units, are a major class of biopolymers essential to all known living organisms. To better understand their…”
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Mapping the Chemical Space of the RNA Cleavage and Its Implications for Ribozyme Catalysis by Mlýnský, Vojtěch, Kührová, Petra, Jurečka, Petr, Šponer, Jiří, Otyepka, Michal, Banáš, Pavel

“…Ribozymes utilize diverse catalytic strategies. We report systematic quantum chemical calculations mapping the catalytic space of RNA cleavage by comparing all…”
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Computer Folding of RNA Tetraloops? Are We There Yet? by Kührová, Petra, Banáš, Pavel, Best, Robert B, Šponer, Jiří, Otyepka, Michal

“…RNA hairpin loops represent important RNA motifs with indispensable biological functions in RNA folding and tertiary interactions, with the 5′-UNCG-3′ and…”
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Simulations of A‑RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration by Beššeová, Ivana, Banáš, Pavel, Kührová, Petra, Košinová, Pavlína, Otyepka, Michal, Šponer, Jiří

“…We have carried out an extended reference set of explicit solvent molecular dynamics simulations (63 simulations with 8.4 μs of simulation data) of canonical…”
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Correction to “Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions” by Kührová, Petra, Mlýnský, Vojtěch, Zgarbová, Marie, Krepl, Miroslav, Bussi, Giovanni, Best, Robert B, Otyepka, Michal, Šponer, Jiří, Banáš, Pavel

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