Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study. - Anna Bochicchio; Miroslav Krepl; Fan Yang; Gabriele Varani; Jirí Sponer; Paolo Carloni (PLoS Comput. Biol., 2018)

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)

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)

How Binding Site Flexibility Promotes RNA Scanning by TbRGG2 RRM: A Molecular Dynamics Simulation Study. - Toon Lemmens; Jirí Sponer; Miroslav Krepl (J. Chem. Inf. Model., 2025)