119 citations · 230 across the 3 of their papers we have counts for
4 papers
Combining simulations and solution experiments as a paradigm for RNA force field refinement
Andrea Cesari, Alejandro Gil-Ley, Giovanni Bussi
Recent computational efforts have shown that the current potential energy models used in molecular dynamics are not accurate enough to describe the conformational ensemble of RNA o…
Empirical corrections to the Amber RNA force field with Target Metadynamics
Alejandro Gil-Ley, Sandro Bottaro, Giovanni Bussi
The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement betw…
RNA Folding Pathways in Stop Motion
Sandro Bottaro, Alejandro Gil-Ley, Giovanni Bussi
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensi…
Enhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering
Alejandro Gil-Ley, Giovanni Bussi
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce…