prof. RNDr. Jiří Šponer, DrSc.

2025

• How Binding Site Flexibility Promotes RNA Scanning by TbRGG2 RRM: A Molecular Dynamics Simulation Study

  LEMMENS Toon ŠPONER Jiří KREPL Miroslav

  Article in Periodical

  Journal of Chemical Information and Modeling, year: 2025, volume: 65, edition: 2, DOI

• The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance

  LEMMENS Toon MLÝNSKÝ Vojtěch ŠPONER Jiří PYKAL Martin BANÁŠ Pavel OTYEPKA Michal KREPL Miroslav

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2025, volume: 21, edition: 24, DOI

2024

• Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes

  KNAPPEOVÁ Barbora MLÝNSKÝ Vojtěch PYKAL Martin ŠPONER Jiří BANÁŠ Pavel OTYEPKA Michal KREPL Miroslav

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2024, volume: 20, edition: 15, DOI

• Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations

  ZHANG Zhengyue MLÝNSKÝ Vojtěch KREPL Miroslav ŠPONER Jiří STADLBAUER Petr

  Article in Periodical

  Journal of Chemical Information and Modeling, year: 2024, volume: 64, edition: 9, DOI

2023

• Atomistic Picture of Opening–Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations

  ZHANG Zhengyue ŠPONER Jiří BUSSI Giovanni MLÝNSKÝ Vojtěch ŠULC Petr SIMMONS Chad R. STEPHANOPOULOS Nicholas KREPL Miroslav

  Article in Periodical

  Journal of Chemical Information and Modeling, year: 2023, volume: 63, edition: 9, DOI

• Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA

  VÖGELE Jennifer ZHANG Zhengyue DUCHARDT-FERNER Elke KRUSE Holger ZHANG Zhengyue ŠPONER Jiří KREPL Miroslav WÖHNERT Jens

  Article in Periodical

  RNA, year: 2023, volume: 29, edition: 6, DOI

2022

• Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS-RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations

  POKORNÁ Pavlína KREPL Miroslav CAMPAGNE Sébastien ŠPONER Jiří

  Article in Periodical

  Journal of Physical Chemistry B, year: 2022, volume: 126, edition: 45, DOI

• Lone-pair...π Contacts in Nucleic Acids: Revision of Lennard-Jones Parameters Needed

  MRÁZIKOVÁ Klaudia AUFFINGER Pascal ŠPONER Jiří KRUSE Holger

  Conference abstract

  Year: 2022, type: Conference abstract

• Photoinduced water-chromophore electron transfer causes formation of guanosine photodamage

  JANICKI Mikolaj J. SZABLA Rafal Kazimierz ŠPONER Jiří GORA Robert W.

  Article in Periodical

  Physical Chemistry Chemical Physics, year: 2022, volume: 24, edition: 14, DOI

• Quantum chemistry reveals AMBER force field shortcomings for anion…π contacts in nucleic acids

  MRÁZIKOVÁ Klaudia AUFFINGER Pascal KRUSE Holger MLÝNSKÝ Vojtěch ŠPONER Jiří

  Conference abstract

  Year: 2022, type: Conference abstract