RNDr. Miroslav Krepl, Ph.D.

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

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

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

• Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field

  KREPL Miroslav POKORNÁ Pavlína MLÝNSKÝ Vojtěch STADLBAUER Petr ŠPONER Jiří

  Article in Periodical

  Nucleic Acids Research, year: 2022, volume: 50, edition: 21, DOI

2021

• Residues flanking the ARK^me3T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations

  POKORNÁ Pavlína KREPL Miroslav ŠPONER Jiří

  Article in Periodical

  Biochimica et Biophysica Acta - General Subjects, year: 2021, volume: 1865, edition: 1, DOI

2019

• Atomic Details on Protein-Protein Recognition - Role of Side Chain Dynamics in Binding Between HP1 and H3 Proteins

  POKORNÁ Pavlína ŠPONER Jiří KREPL Miroslav BÁRTOVÁ Eva

  Conference abstract

  Year: 2019, type: Conference abstract

• DNA Damage Changes Distribution Pattern and Levels of HP1 Protein Isoforms in the Nucleolus and Increases Phosphorylation of HP1 beta-Ser88

  LEGARTOVÁ Sofia LOCHMANOVÁ Gabriela ZDRÁHAL Zbyněk KOZUBEK Stanislav ŠPONER Jiří KREPL Miroslav POKORNÁ Pavlína BÁRTOVÁ Eva

  Article in Periodical

  CELLS, year: 2019, volume: 8, edition: 9, DOI

• QM/MM Calculations on Protein-RNA Complexes: Understanding Limitations of Classical MD Simulations and Search for Reliable Cost-Effective QM Methods.

  POKORNÁ Pavlína KREPL Miroslav ŠPONER Jiří MRÁZIKOVÁ Klaudia MLYNSKY Vojech KRUSE Holger

  Conference abstract

  Year: 2019, type: Conference abstract

• Role of Fine Structural Dynamics in Recognition of Histone H3 by HP1 gamma(CSD) Dimer and Ability of Force Fields to Describe Their Interaction Network

  POKORNÁ Pavlína KREPL Miroslav BARTOVA E. ŠPONER Jiří

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2019, volume: 15, edition: 10, DOI

2018

• QM/MM Calculations on Protein-RNA Complexes: Understanding Limitations of Classical MD Simulations and Search for Reliable Cost-Effective QM Methods

  POKORNÁ Pavlína KRUSE Holger KREPL Miroslav ŠPONER Jiří

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2018, volume: 14, edition: 10, DOI