Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose···Nucleobase Lone-Pair···π Contacts in Nucleic Acids. - Klaudia Mráziková; Jirí Sponer; Vojtech Mlýnský; Pascal Auffinger; Holger Kruse (J. Chem. Inf. Model., 2021)

Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions. - Klaudia Mráziková; Holger Kruse; Vojtech Mlýnský; Pascal Auffinger; Jirí Sponer (J. Chem. Inf. Model., 2022)

Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes. - Petra Kührová; Vojtech Mlýnský; Michal Otyepka; Jirí Sponer; Pavel Banás (J. Chem. Inf. Model., 2023)

Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. - Zhengyue Zhang; Jirí Sponer; Giovanni Bussi; Vojtech Mlýnský; Petr Sulc; Chad R. Simmons; Nicholas Stephanopoulos; Miroslav Krepl (J. Chem. Inf. Model., 2023)

Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations. - Petr Stadlbauer; Vojtech Mlýnský; Miroslav Krepl; Jirí Sponer (J. Chem. Inf. Model., 2023)

Correction to "Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes". - Petra Kührová; Vojtech Mlýnský; Michal Otyepka; Jirí Sponer; Pavel Banás (J. Chem. Inf. Model., 2024)

Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. - Zhengyue Zhang; Vojtech Mlýnský; Miroslav Krepl; Jirí Sponer; Petr Stadlbauer (J. Chem. Inf. Model., 2024)

Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space. - Michal Janecek; Petra Kührová; Vojtech Mlýnský; Petr Stadlbauer; Michal Otyepka; Giovanni Bussi; Jirí Sponer; Pavel Banás (J. Comput. Chem., 2025)