G. Bussi

Exploration, representation and rationalization of the conformational phase-space of N-glycans

The paper explores the conformational phase-space of N-glycans using enhanced sampling and dimensionality reduction to identify key torsion angles and their biological relevance.

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.

Arginine multivalency stabilizes protein/RNA condensates

This study uses molecular dynamics simulations to show that arginine stabilizes protein/RNA condensates more effectively than lysine due to its multivalency.

Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations

This study predicts the 3D structures and dynamics of five RNA stem loops in the SARS-CoV-2 5' UTR using molecular dynamics simulations and enhanced sampling techniques.

Directional translocation resistance of Zika xrRNA

The paper investigates how xrRNA from flaviviruses resists degradation by exonucleases while being unwound by replicases, revealing a directional mechanism of stress propagation.

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.

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.

Conformational Ensemble of RNA Oligonucleotides from Reweighted Molecular Simulations

The paper determines the conformational ensemble of RNA tetranucleotides using NMR data and molecular dynamics simulations with a reweighting scheme.