M. Otyepka

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

The paper adjusts the AMBER OL3 force field to improve RNA simulations by fixing intra-nucleotide steric clashes in base-phosphate interactions.

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

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.

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

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

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

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.

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

This study analyzes MD simulations of the UNCG RNA tetraloop, identifying force field deficiencies that contribute to its instability in simulations.

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

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.

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

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.

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

This paper improves the AMBER RNA force field by tuning hydrogen-bonding interactions to better match experimental data in RNA folding simulations.