RNDr. Miroslav Krepl, Ph.D.
Total number of publications: 28
2022
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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, year: 2022, volume: 126, edition: 45, DOI
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Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field
Nucleic Acids Research, year: 2022, volume: 50, edition: 21, DOI
2021
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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, year: 2021, volume: 1865, edition: 1, DOI
2019
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Atomic Details on Protein-Protein Recognition - Role of Side Chain Dynamics in Binding Between HP1 and H3 Proteins
Year: 2019, type: Conference abstract
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DNA Damage Changes Distribution Pattern and Levels of HP1 Protein Isoforms in the Nucleolus and Increases Phosphorylation of HP1 beta-Ser88
CELLS, year: 2019, volume: 8, edition: 9, DOI
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QM/MM Calculations on Protein-RNA Complexes: Understanding Limitations of Classical MD Simulations and Search for Reliable Cost-Effective QM Methods.
Year: 2019, type: Conference abstract
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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, year: 2019, volume: 15, edition: 10, DOI
2018
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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, year: 2018, volume: 14, edition: 10, DOI
2017
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Aromatic side-chain conformational switch on the surface of the RNA Recognition Motif enables RNA discrimination
NATURE COMMUNICATIONS, year: 2017, volume: 8, DOI
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Coordination between the polymerase and RNase H activity of HIV-1 reverse transcriptase
Nucleic Acids Research, year: 2017, volume: 45, edition: 6, DOI