J. Sponer

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.

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.

Z-DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA torsions for AMBER

The paper improves AMBER force fields by refining gamma DNA torsions to better describe Z-DNA and non-canonical DNA structures.

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.

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.

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.

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.

Primitive RNA-catalysis with guanine-rich oligonucleotide sequences - the case of a (GGC)3 nonamer

The paper investigates the catalytic potential of a (GGC)3 nonamer by showing thermal treatment produces a (GGC)3G species and supports transient geometries compatible with terminal recombination chemistry.

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.

Local-to-global signal transduction at the core of the Mn2+ sensing riboswitch

The paper investigates the Mn2+ sensing yybP-ykoY riboswitch, revealing how local structural changes trigger global signal transduction through RNA dynamics.

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.