Author
Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.
8 papers
Recent·Most cited
Z. Zhang, V. Mlynsky, M. Krepl, J. Sponer, P. Stadlbauer
This study uses pulling simulations to analyze the mechanical stability and unfolding pathways of tetrameric parallel G-quadruplexes, identifying key factors like vertical force components and unfolding transitions.
bioRxiv · Jan 26, 2024Biophysics
V. Mlynsky, P. Kuhrova, P. Stadlbauer, M. Krepl, M. Otyepka, P. Banas, J. Sponer
The paper adjusts the AMBER OL3 force field to improve RNA simulations by fixing intra-nucleotide steric clashes in base-phosphate interactions.
bioRxiv · Sep 5, 2023 · PreprintBiophysics
P. Stadlbauer, V. Mlynsky, M. Krepl, J. Sponer
The paper uses atomistic simulations to study how human telomeric GQs unfold under different mechanical forces and identifies factors influencing their unfolding mechanisms.
bioRxiv · Jan 27, 2023Biophysics
V. Mlynsky, M. Janecek, P. Kuhrova, T. Frohlking, M. Otyepka, G. Bussi, P. Banas, J. Sponer
This study compares enhanced sampling techniques and force field corrections for RNA tetraloop folding simulations, finding that combining REST2 with ST-MetaD improves sampling efficiency and that force field modifications stabilize native states.
bioRxiv · Nov 30, 2021 · PreprintBiophysics
M. Janecek, P. Kuhrova, V. Mlynsky, M. Otyepka, J. Sponer, P. Banas
The paper improves the RESP charge model to better describe electrostatic potentials around molecules, particularly for aromatic heterocyclic compounds, enhancing nucleic acid force field performance.
bioRxiv · Sep 14, 2020Biophysics
K. Mrazikova, V. Mlynsky, P. Kuhrova, P. Pokorna, H. Kruse, M. Krepl, M. Otyepka, P. Banas, J. Sponer
This study analyzes MD simulations of the UNCG RNA tetraloop, identifying force field deficiencies that contribute to its instability in simulations.
bioRxiv · Jul 27, 2020 · PreprintBiophysics
V. Mlynsky, P. Kuhrova, T. Kuhr, M. Otyepka, G. Bussi, P. Banas, J. Sponer
The paper improves RNA force field simulations by adding two terms, gHBfix and tHBfix, to better model terminal nucleotide interactions and enhance accuracy for RNA tetranucleotides.
bioRxiv · Mar 8, 2020Biophysics
P. Kuhrova, V. Mlynsky, M. Zgarbova, M. Krepl, G. Bussi, R. B. Best, M. Otyepka, J. Sponer, P. Banas
This paper improves the AMBER RNA force field by tuning hydrogen-bonding interactions to better match experimental data in RNA folding simulations.
bioRxiv · Jan 18, 2019Biochemistry