| QM/MM calculations on protein–RNA complexes: Understanding limitations of classical MD simulations and search for reliable cost-effective QM methods P Pokorna, H Kruse, M Krepl, J Sponer Journal of chemical theory and computation 14 (10), 5419-5433, 2018 | 38 | 2018 |
| UUCG RNA tetraloop as a formidable force-field challenge for MD simulations K Mráziková, V Mlýnský, P Kührová, P Pokorná, H Kruse, M Krepl, ... Journal of chemical theory and computation 16 (12), 7601-7617, 2020 | 35 | 2020 |
| Recognition of N6-methyladenosine by the YTHDC1 YTH domain studied by molecular dynamics and NMR spectroscopy: the role of hydration M Krepl, FF Damberger, C von Schroetter, D Theler, P Pokorná, ... The Journal of Physical Chemistry B 125 (28), 7691-7705, 2021 | 18 | 2021 |
| MD and QM/MM Study of the Quaternary HutP Homohexamer Complex with mRNA, l-Histidine Ligand, and Mg2+ P Pokorna, M Krepl, H Kruse, J Sponer Journal of Chemical Theory and Computation 13 (11), 5658-5670, 2017 | 17 | 2017 |
| Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field M Krepl, P Pokorná, V Mlýnský, P Stadlbauer, J Šponer Nucleic acids research 50 (21), 12480-12496, 2022 | 15 | 2022 |
| DNA damage changes distribution pattern and levels of HP1 protein isoforms in the nucleolus and increases phosphorylation of HP1β-Ser88 S Legartová, G Lochmanová, Z Zdráhal, S Kozubek, J Šponer, M Krepl, ... Cells 8 (9), 1097, 2019 | 11 | 2019 |
| Conformational heterogeneity of RNA stem-loop hairpins bound to FUS-RNA recognition motif with disordered RGG tail revealed by unbiased molecular dynamics simulations P Pokorná, M Krepl, S Campagne, J Sponer The Journal of Physical Chemistry B 126 (45), 9207-9221, 2022 | 7 | 2022 |
| Residues flanking the ARKme3T/S motif allow binding of diverse targets to the HP1 chromodomain: insights from molecular dynamics simulations P Pokorná, M Krepl, J Šponer Biochimica et Biophysica Acta (BBA)-General Subjects 1865 (1), 129771, 2021 | 3 | 2021 |
| Parallel G-quadruplex folds via multiple paths involving G-tract stacking and structuring from coil ensemble P Pokorna, V Mlynsky, G Bussi, J Sponer, P Stadlbauer bioRxiv, 2023.09. 09.556957, 2023 | 2 | 2023 |
| Role of Fine Structural Dynamics in Recognition of Histone H3 by HP1γ (CSD) Dimer and Ability of Force Fields to Describe Their Interaction Network P Pokorná, M Krepl, E Bártová, J Šponer Journal of Chemical Theory and Computation 15 (10), 5659-5673, 2019 | 2 | 2019 |
| Molecular dynamics simulations reveal the parallel stranded d (GGGA) 3GGG DNA quadruplex folds via multiple paths from a coil-like ensemble P Pokorná, V Mlýnský, G Bussi, J Šponer, P Stadlbauer International Journal of Biological Macromolecules 261, 129712, 2024 | | 2024 |
| Structural dynamics of biomolecular complexes P Pokorná | | |
