Výpis publikací

LEMMENS, Toon; Jiří ŠPONER a Miroslav KREPL. How Binding Site Flexibility Promotes RNA Scanning by TbRGG2 RRM: A Molecular Dynamics Simulation Study. Journal of Chemical Information and Modeling. American Chemical Society, 2025, roč. 65, č. 2, s. 896-907. ISSN 1549-9596. Dostupné z: https://doi.org/10.1021/acs.jcim.4c01954.

LEMMENS, Toon; Vojtěch MLÝNSKÝ; Jiří ŠPONER; Martin PYKAL; Pavel BANÁŠ; Michal OTYEPKA a Miroslav KREPL. The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance. Journal of Chemical Theory and Computation. AMER CHEMICAL SOC, 2025, roč. 21, č. 24, s. 12796-12809. ISSN 1549-9618. Dostupné z: https://doi.org/10.1021/acs.jctc.5c00776.

KNAPPEOVÁ, Barbora; Vojtěch MLÝNSKÝ; Martin PYKAL; Jiří ŠPONER; Pavel BANÁŠ; Michal OTYEPKA a Miroslav KREPL. Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes. Journal of Chemical Theory and Computation. WASHINGTON: American Chemical Society, 2024, roč. 20, č. 15, s. 6917-6929. ISSN 1549-9618. Dostupné z: https://doi.org/10.1021/acs.jctc.4c00601.

POKORNÁ, Pavlína; Miroslav KREPL; Sébastien CAMPAGNE a Jiří ŠPONER. Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS-RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations. Journal of Physical Chemistry B. American Chemical Society, 2022, roč. 126, č. 45, s. 9207-9221. ISSN 1520-6106. Dostupné z: https://doi.org/10.1021/acs.jpcb.2c06168.

KREPL, Miroslav; Pavlína POKORNÁ; Vojtěch MLÝNSKÝ; Petr STADLBAUER a Jiří ŠPONER. Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field. Nucleic Acids Research. Oxford University Press, 2022, roč. 50, č. 21, s. 12480-12496. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkac1106.

POKORNÁ, Pavlína; Miroslav KREPL a Jiří ŠPONER. Residues flanking the ARK^me3T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations. Biochimica et Biophysica Acta - General Subjects. Amsterdam: Elsevier B.V., 2021, roč. 1865, č. 1, s. 1-12. ISSN 0304-4165. Dostupné z: https://doi.org/10.1016/j.bbagen.2020.129771.

POKORNÁ, Pavlína; Jiří ŠPONER; Miroslav KREPL a Eva BÁRTOVÁ. Atomic Details on Protein-Protein Recognition - Role of Side Chain Dynamics in Binding Between HP1 and H3 Proteins. In PhD Joint Retreat. 2019. ISBN 978-80-210-9301-0.

LEGARTOVÁ, Sofia; Gabriela LOCHMANOVÁ; Zbyněk ZDRÁHAL; Stanislav KOZUBEK; Jiří ŠPONER; Miroslav KREPL; Pavlína POKORNÁ a Eva BÁRTOVÁ. DNA Damage Changes Distribution Pattern and Levels of HP1 Protein Isoforms in the Nucleolus and Increases Phosphorylation of HP1 beta-Ser88. CELLS. 2019, roč. 8, č. 9, s. "1097", 22 s. ISSN 2073-4409. Dostupné z: https://doi.org/10.3390/cells8091097.

POKORNÁ, Pavlína; Miroslav KREPL; Jiří ŠPONER; Klaudia MRÁZIKOVÁ; Vojech MLYNSKY a Holger KRUSE. QM/MM Calculations on Protein-RNA Complexes: Understanding Limitations of Classical MD Simulations and Search for Reliable Cost-Effective QM Methods. In RNA 2019. 2019.

POKORNÁ, Pavlína; Miroslav KREPL; E. BARTOVA a Jiří ŠPONER. 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. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2019, roč. 15, č. 10, s. 5659-5673. ISSN 1549-9618. Dostupné z: https://doi.org/10.1021/acs.jctc.9b00434.

POKORNÁ, Pavlína; Holger KRUSE; Miroslav KREPL a Jiří ŠPONER. QM/MM Calculations on Protein-RNA Complexes: Understanding Limitations of Classical MD Simulations and Search for Reliable Cost-Effective QM Methods. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2018, roč. 14, č. 10, s. 5419-5433. ISSN 1549-9618. Dostupné z: https://doi.org/10.1021/acs.jctc.8b00670.

DIARRA DIT KONTÉ, Nana; Miroslav KREPL; Fred DAMBERGER; N RIPPIN; O DUSS; Jiří ŠPONER a Allain FRÉDÉRIC. Aromatic side-chain conformational switch on the surface of the RNA Recognition Motif enables RNA discrimination. NATURE COMMUNICATIONS. Nature Publishing Group, 2017, roč. 8, s. e654. ISSN 2041-1723. Dostupné z: https://doi.org/10.1038/s41467-017-00631-3.

FIGIEL, M; Miroslav KREPL; J POZNANSKI; A GOTAB; Jiří ŠPONER a Marcin NOWOTNY. Coordination between the polymerase and RNase H activity of HIV-1 reverse transcriptase. Nucleic Acids Research. Oxford: Oxford University Press, 2017, roč. 45, č. 6, s. 3341-3352. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkx004.

ŠPONER, Jiří; Miroslav KREPL; Pavel BANÁŠ; P KUHROVA; Marie ZGARBOVÁ; Petr JUREČKA; Marek HAVRILA a Michal OTYEPKA. How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes? Wiley Interdisciplinary Reviews: RNA. Hoboken, USA: WILEY-BLACKWELL, 2017, roč. 8, č. 3, 17 s. ISSN 1757-7004. Dostupné z: https://doi.org/10.1002/wrna.1405.

POKORNÁ, Pavlína; Miroslav KREPL; Holger KRUSE a Jiří ŠPONER. MD and QM/MM Study of the Quaternary HutP Homohexamer Complex with mRNA, L-Histidine Ligand, and Mg2+. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2017, roč. 13, č. 11, s. 5658-5670. ISSN 1549-9618. Dostupné z: https://doi.org/10.1021/acs.jctc.7b00598.

HAVRILA, Marek; Marie ZGARBOVÁ; Petr JURECKA; Pavel BANÁŠ; Miroslav KREPL; Michal OTYEPKA a Jiri ŠPONER. MD Simulations of HIV‐1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases. In 22nd Annual Meeting of the RNA Society. 2017.

KREPL, Miroslav; Markus BLATTER; Antoine CLERY; Fred F DAMBERGER; Frederic H T ALLAIN a Jiří ŠPONER. Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition. Nucleic acids research. Oxford University Press, 2017. ISSN 1362-4962. Dostupné z: https://doi.org/10.1093/nar/gkx418.

KREPL, Miroslav; Antoine CLERY; Markus BLATTER; Frederic ALLAIN a Jiří ŠPONER. Study of Fox-1 and SRSF1 RRMs - the molecular recognition and hydration. In 22nd Annual Meeting of the RNA Society. 2017.

KREPL, Miroslav; Antoine CLERY; Markus BLATTER; Frederic H. T. ALLAIN a Jiří ŠPONER. Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs. Nucleic Acids Research. Oxford: Oxford University Press, 2016, roč. 44, č. 13, s. 6452-6470. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkw438.

KREPL, Miroslav; Marek HAVRILA; Petr STADLBAUER; Pavel BANÁŠ; Michal OTYEPKA; Josef PASULKA; Richard ŠTEFL a Jiří ŠPONER. Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes? Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2015, roč. 11, č. 3, s. 1220-1243. ISSN 1549-9618. Dostupné z: https://doi.org/10.1021/ct5008108.

ISLAM, Barira; Petr STADLBAUER; Miroslav KREPL; Jaroslav KOČA; Stephen NEIDLE; Shozeb HAIDER a Jiří ŠPONER. Extended molecular dynamics of a c-kit promoter quadruplex. Nucleic Acids Research. Oxford: Oxford University Press, 2015, roč. 43, č. 18, s. 8673-8693. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkv785.

HAVRILA, Marek; Marie ZGARBOVÁ; Petr JUREČKA; Pavel BANÁŠ; Miroslav KREPL; Michal OTYEPKA a Jiří ŠPONER. Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields. Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2015, roč. 119, č. 49, s. 15176-15190. ISSN 1520-6106. Dostupné z: https://doi.org/10.1021/acs.jpcb.5b08876.

ESTARELLAS MARTIN, Carolina; Michal OTYEPKA; Jaroslav KOČA; Pavel BANÁŠ; Miroslav KREPL a Jiří ŠPONER. Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS. AMSTERDAM: ELSEVIER SCIENCE BV, 2015, roč. 1850, č. 5, s. 1072-1090. ISSN 0304-4165. Dostupné z: https://doi.org/10.1016/j.bbagen.2014.10.021.

ŠPONER, Jiří; Pavel BANÁŠ; Petr JUREČKA; Marie ZGARBOVÁ; Petra KÜHROVÁ; Marek HAVRILA; Miroslav KREPL; Petr STADLBAUER a Michal OTYEPKA. Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome. The Journal of Physical Chemistry Letters. Washington: American Chemical Society, 2014, roč. 5, č. 10, s. 1771-1782. ISSN 1948-7185. Dostupné z: https://doi.org/10.1021/jz500557y.

MLÁDEK, Arnošt; Miroslav KREPL; Daniel SVOZIL; Petr CECH; Michal OTYEPKA; Pavel BANÁŠ; Marie ZGARBOVA; Petr JURECKA a Jiří ŠPONER. Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory. Physical Chemistry Chemical Physics. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2013, roč. 15, č. 19, s. 7295-7310. ISSN 1463-9076. Dostupné z: https://doi.org/10.1039/c3cp44383c.

KREPL, Miroslav; Kamila RÉBLOVÁ; Jaroslav KOČA a Jiří ŠPONER. Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-turns, Loops, and Tetraloops. JOURNAL OF PHYSICAL CHEMISTRY B. Washington: American Chemical Society, 2013, roč. 117, č. 18, s. 5540-5555. ISSN 1520-6106. Dostupné z: https://doi.org/10.1021/jp401482m.

KREPL, Miroslav; Michal OTYEPKA; Pavel BANÁŠ a Jiří ŠPONER. Effect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration Study. JOURNAL OF PHYSICAL CHEMISTRY B. Washington: American Chemical Society, 2013, roč. 117, č. 6, s. 1872-1879. ISSN 1520-6106. Dostupné z: https://doi.org/10.1021/jp311180u.

STADLBAUER, Petr; Miroslav KREPL; Thomas E. CHEATHAM; Jaroslav KOČA a Jiří ŠPONER. Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations. Nucleic Acids Research. Oxford, UK: Oxford Press, 2013, roč. 41, č. 14, s. 7128-7143. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkt412.

KREPL, Miroslav a Marek HAVRILA. Study of protein/RNA systems utilizing NMR structural data. In RNA-methods workshop. 2013.

KREPL, Miroslav; Marie ZGARBOVA; Petr STADLBAUER; Michal OTYEPKA; Pavel BANÁŠ; Jaroslav KOČA; Thomas E. CHEATHAM; Petr JURECKA a Jiří ŠPONER. Reference Simulations of Noncanonical Nucleic Acids with Different chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA. Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2012, roč. 8, č. 7, s. 2506-2520. ISSN 1549-9618. Dostupné z: https://doi.org/10.1021/ct300275s.

KREPL, Miroslav; Kamila RÉBLOVÁ a Jiří ŠPONER. Molecular dynamics of ribosomal L1 stalk. In Dynamics of Protein-Nucleic Acid Interactions: Integrating Simulations with Experiments. 2011.