Magnesium ions are essential for RNA structure but difficult to model due to slow binding kinetics and experimental limitations. We present an enhanced-sampling strategy that accelerates Mg$^{2+}$ inn...

Structural ensemble refinement is widely used to integrate molecular simulations with experimental measurements. While most applications focus on the maximum-a-posteriori (MAP) ensemble, Bayesian samp...

Authored by Giovanni Bussi

Although electrolyte density measurements have been reported for over a century, employing them to obtain accurate partial molar volume (PMV) profiles as a function of salt concentration has remained ...

Exploring RNA Dynamics across Scales

RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in di...

PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. Whi...

9th Workshop

9th Workshop

9th Workshop

A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms

The function of RNA molecules is deeply related to their secondary structure, which determines which nucleobases are accessible for pairing. Most RNA molecules however function through dynamic and het...

Exploring RNA Dynamics across Scales

Biomolecules rely on water and ions for stable folding, but these interactions are often transient, dynamic, or disordered and thus hidden from experiments and evaluation challenges that represent bi....

Predicting the secondary structure of RNA is a core challenge in computational biology, essential for understanding molecular function and designing novel therapeutics. The field has evolved from foun...

PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. Whi...

Biomolecules rely on water and ions for stable folding, but these interactions are often transient, dynamic, or disordered and thus hidden from experiments and evaluation challenges that represent bio...

YouTube video by CASP RNA SIG

Welcome nucleic acid enthusiasts to the Special Interest Group (SIG) focused different aspects of nucleic acid 3D structure prediction, including but not limited to obtaining experimental data, buildi...

Investigating structural variability is essential for understanding protein biological functions. Although AlphaFold2 accurately predicts static structures, it fails to capture the full spectrum of f...

Authored by Giovanni Bussi and 1 other author

RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in di...

Abstract. Adenosine-to-inosine (A-to-I) editing is a highly abundant modification of double-stranded RNA (dsRNA) and plays an important role in posttranscr