Author

M. Otyepka

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 8 Biochemistry· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 6 Research Focus:protein folding & dynamics· 4 Research Focus:benchmarking· 3 Approach:deep learning· 3 Assay:DNA methylation· 2 Approach:mechanistic / dynamical model· 2 Assay:multiome· 2 Research Focus:protein structure prediction· 2

Frequent Co-Authors

J. Sponer· 9 shared P. Banas· 7 shared V. Mlynsky· 7 shared P. Kuhrova· 6 shared M. Krepl· 4 shared G. Bussi· 3 shared P. Stadlbauer· 3 shared B. Islam· 2 shared

Activity by Year

2019-2024 · peak 5/yr

Co-Author Collaboration Network

10 top collaborators · 30 mutual co-author links

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9 shared papersBiophysics

J. Sponer

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Author profile →

9 papers

Recent·Most cited

Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes

B. Knappeova, V. Mlynsky, M. Pykal, J. Sponer, P. Banas, M. Otyepka, M. Krepl

This study benchmarks force-field performance for DNA/RNA hybrid duplexes, finding no force field accurately reproduces all structural features and highlighting parameter conflicts.

bioRxiv · May 6, 2024Biophysics

Simple Adjustment of Intra-nucleotide Base-phosphate Interaction in OL3 AMBER Force Field Improves RNA Simulations

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

Towards Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Corrections

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

Insights into G-Quadruplex-Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding

P. Stadlbauer, B. Islam, M. Otyepka, J. Chen, D. Monchaud, J. Zhou, J.-L. Mergny, J. Sponer

This study uses atomistic simulations to investigate G4-hemin interactions, revealing dynamic binding mechanisms and suggesting hemin's role in G4 folding.

bioRxiv · Nov 9, 2020Biophysics

W-RESP: Well-Restrained Electrostatic Potential Derived Charges. Revisiting the Charge Derivation Model.

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

UNCG RNA tetraloop as a formidable force-field challenge for MD simulations

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

Fine-tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides

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

Stability of Two-quartet G-quadruplexes and Their Dimers in Atomistic Simulations

B. Islam, P. Stadlbauer, M. Vorlickova, J.-L. Mergny, M. Otyepka, J. Sponer

This study uses molecular dynamics simulations to investigate the stability of two-quartet and four-quartet G-quadruplexes, finding that three quartets are needed for stable DNA GQs and RNA two-quartet GQs are weakly stable.

bioRxiv · Feb 25, 2020Biophysics

IMPROVING THE PERFORMANCE OF THE AMBER RNA FORCE FIELD BY TUNING THE HYDROGEN-BONDING INTERACTIONS

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