M. Krepl

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

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

The Drosophila RNA binding protein Hrp48 binds a specificRNA sequence of the msl-2 mRNA 3' UTR to regulatetranslation

This paper identifies the RNA binding specificity of Hrp48, showing it binds the msl-2 mRNA 3' UTR independently of Sxl and Unr downstream of their binding sites.

Mechanical stability and unfolding pathways of parallel tetrameric G-quadruplexes probed by pulling simulations

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.

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.

Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations

The paper uses atomistic simulations to study how human telomeric GQs unfold under different mechanical forces and identifies factors influencing their unfolding mechanisms.

Recognition of N6-methyladenosine by the YTHDC1 YTH domain studied by molecular dynamics and NMR spectroscopy: The role of hydration

This study investigates how YTHDC1 recognizes m6A through molecular dynamics, NMR, and ITC, showing that hydration and water networks are critical for m6A selectivity.

Phosphorothioate Substitutions in RNA Structure Studied by Molecular Dynamics Simulations, QM/MM Calculations and NMR Experiments

This study investigates how phosphorothioate substitutions affect RNA structure and dynamics using MD simulations, QM/MM calculations, and NMR experiments on a riboswitch model.

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.

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.