V. Mlýnský

发表

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

J. Šponer, M. Otyepka, P. Banáš, 2020, bioRxiv.

Improving the Performance of the RNA Amber Force Field by Tuning the Hydrogen-Bonding Interactions

J. Šponer, G. Bussi, R. Best, 2018, bioRxiv.

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

J. Šponer, M. Otyepka, P. Banáš, 2020, bioRxiv.

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

J. Šponer, G. Bussi, M. Otyepka, 2020, bioRxiv.

Mapping the Chemical Space of the RNA Cleavage and Its Implications for Ribozyme Catalysis.

J. Šponer, M. Otyepka, P. Banáš, 2017, The journal of physical chemistry. B.

Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field

J. Šponer, G. Bussi, P. Banáš, 2022, Journal of chemical theory and computation.

Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field

J. Šponer, M. Krepl, V. Mlýnský, 2022, bioRxiv.

Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions

J. Šponer, P. Auffinger, H. Kruse, 2022, J. Chem. Inf. Model..

The role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations.

Michal Otyepka, Pavel Banáš, Jiří Šponer, 2015, Physical chemistry chemical physics : PCCP.

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

J. Šponer, M. Otyepka, P. Banáš, 2021, Journal of chemical theory and computation.

Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions.

J. Šponer, G. Bussi, R. Best, 2019, Journal of chemical theory and computation.

Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.

K. Réblová, J. Šponer, N. Walter, 2010, The journal of physical chemistry. B.

Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose···Nucleobase Lone-Pair···π Contacts in Nucleic Acids

J. Šponer, P. Auffinger, H. Kruse, 2021, J. Chem. Inf. Model..

Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications.

J. Šponer, G. Bussi, M. Otyepka, 2022, Journal of chemical theory and computation.

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

J. Šponer, G. Bussi, M. Otyepka, 2021, bioRxiv.

UUCG RNA Tetraloop as a Formidable Force-Field Challenge for MD Simulations.

J. Šponer, M. Otyepka, P. Banáš, 2020, Journal of chemical theory and computation.

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

J. Šponer, G. Bussi, M. Otyepka, 2020, bioRxiv.

Correction to "Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions".

J. Šponer, G. Bussi, R. Best, 2019, Journal of chemical theory and computation.

Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides.

Giovanni Bussi, G. Bussi, V. Mlýnský, 2017, RNA.

Reactive conformation of the active site in the hairpin ribozyme achieved by molecular dynamics simulations with ε/ζ force field reparametrizations.

J. Šponer, N. Walter, M. Otyepka, 2015, The journal of physical chemistry. B.

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme.

Adrian J Mulholland, Michal Otyepka, Pavel Banáš, 2014, Journal of chemical theory and computation.

Atomistic Picture of Opening–Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations

J. Šponer, G. Bussi, N. Stephanopoulos, 2023, Journal of chemical information and modeling.

Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility

Giovanni Bussi, G. Bussi, V. Mlýnský, 2017, The journal of physical chemistry letters.

QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms.

J. Šponer, N. Walter, M. Otyepka, 2011, The journal of physical chemistry. B.

Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations

J. Šponer, M. Krepl, V. Mlýnský, 2023, bioRxiv.

Exploring RNA structure and dynamics through enhanced sampling simulations.

Giovanni Bussi, G. Bussi, V. Mlýnský, 2017, Current opinion in structural biology.

Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes

J. Šponer, M. Otyepka, P. Banáš, 2023, J. Chem. Inf. Model..

Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations

J. Šponer, M. Otyepka, P. Banáš, 2023, bioRxiv.

Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations

V. Mlýnský, Miroslav Krepl, Petr Stadlbauer, 2024, bioRxiv.

Molecular dynamics simulations reveal the parallel stranded d(GGGA)3GGG DNA quadruplex folds via multiple paths from a coil-like ensemble.

G. Bussi, V. Mlýnský, Pavlína Pokorná, 2024, International journal of biological macromolecules.

Parallel G-quadruplex folds via multiple paths involving G-tract stacking and structuring from coil ensemble

G. Bussi, V. Mlýnský, Pavlína Pokorná, 2023, bioRxiv.