11 citations · 18 across the 7 of their papers we have counts for
7 papers
Enhanced sampling and cryo-EM data resolve magnesium binding to RNA
Olivier Languin-Cattoën, Elisa Posani, Giovanni Bussi
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 accel…
Bayesian Sampling of Structural Ensembles: The Role of Ensemble-Counting Measures
Ivan Gilardoni, Giovanni Bussi
Structural ensemble refinement is widely used to integrate molecular simulations with experimental measurements. While most applications focus on the maximum-a-posteriori (MAP) ens…
MERGE-RNA: a physics-based model to predict RNA secondary structure ensembles with chemical probing
Giuseppe Sacco, Jianhui Li, Redmond P. Smyth +2
RNA function is tied to secondary structure, operating through dynamic and heterogeneous structural ensembles. While current analysis tools typically output single static structure…
Making PLUMED fly: a tutorial on optimizing performance
Daniele Rapetti, Massimiliano Bonomi, Carlo Camilloni +2
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 dyn…
Machine Learning for RNA Secondary Structure Prediction: a review of current methods and challenges
Giuseppe Sacco, Giovanni Bussi, Guido Sanguinetti
Predicting the secondary structure of RNA is a core challenge in computational biology, essential for understanding molecular function and designing novel therapeutics. The field h…
Molecular simulations matching denaturation experiments for N6-Methyladenosine
Valerio Piomponi, Thorben Fröhlking, Mattia Bernetti +1
Post-transcriptional modifications are crucial for RNA function and can affect its structure and dynamics. Force-field based classical molecular dynamics simulations are a fundamen…
Statistical mechanical properties of sequence space determine the efficiency of the various algorithms to predict interaction energies and native contacts from protein coevolution
G. Franco, M. Cagiada, G. Bussi +1
Studying evolutionary correlations in alignments of homologous sequences by means of an inverse Potts model has proven useful to obtain residue-residue contact energies and to pred…