RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview von Šponer, Jiří, Bussi, Giovanni, Krepl, Miroslav, Banáš, Pavel, Bottaro, Sandro, Cunha, Richard A, Gil-Ley, Alejandro, Pinamonti, Giovanni, Poblete, Simón, Jurečka, Petr, Walter, Nils G, Otyepka, Michal

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Investigations of Stacked DNA Base-Pair Steps: Highly Accurate Stacking Interaction Energies, Energy Decomposition, and Many-Body Stacking Effects von Kruse, Holger, Banáš, Pavel, Šponer, Jiřı́

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Assessing the Current State of Amber Force Field Modifications for DNA von Galindo-Murillo, Rodrigo, Robertson, James C, Zgarbová, Marie, Šponer, Jiří, Otyepka, Michal, Jurečka, Petr, Cheatham, Thomas E

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Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids von Svozil, Daniel, Šponer, Judit E, Marchan, Ivan, Pérez, Alberto, Cheatham, Thomas E, Forti, F, Luque, F. Javier, Orozco, Modesto, Šponer, Jiří

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Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B‑DNA von Zgarbová, Marie, Šponer, Jiří, Otyepka, Michal, Cheatham, Thomas E., Galindo-Murillo, Rodrigo, Jurečka, Petr

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

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High-energy chemistry of formamide: A unified mechanism of nucleobase formation von Ferus, Martin, Nesvorný, David, Šponer, Jiří, Kubelík, Petr, Michalčíková, Regina, Shestivská, Violetta, Šponer, Judit E., Civiš, Svatopluk

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QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin–Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches von Kruse, Holger, Havrila, Marek, Šponer, Jiřı́

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Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters von Zgarbová, Marie, Luque, F. Javier, Šponer, Jiří, Cheatham, Thomas E, Otyepka, Michal, Jurečka, Petr

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

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Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking von Kruse, Holger, Šponer, Jiří

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Z‑DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER von Zgarbova, Marie, Sponer, Jiri, Jurecka, Petr

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

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Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA von Zgarbová, Marie, Otyepka, Michal, Šponer, Jiří, Lankaš, Filip, Jurečka, Petr

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Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations... von Svozil, Daniel, Hobza, Pavel, Šponer, Jiří

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Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G‑Quadruplexes von Havrila, Marek, Stadlbauer, Petr, Islam, Barira, Otyepka, Michal, Šponer, Jiří

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Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations von Stadlbauer, Petr, Mlýnský, Vojtěch, Krepl, Miroslav, Šponer, Jiří

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High-Energy Chemistry of Formamide: A Simpler Way for Nucleobase Formation von Ferus, Martin, Michalčíková, Regina, Shestivská, Violetta, Šponer, Jiří, Šponer, Judit E, Civiš, Svatopluk

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Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS-RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations von Pokorná, Pavlína, Krepl, Miroslav, Campagne, Sébastien, Šponer, Jiří

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

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