74 citations · 112 across the 3 of their papers we have counts for
3 papers
Molecular dynamics simulations with grand-canonical reweighting suggest cooperativity effects in RNA structure probing experiments
Nicola Calonaci, Mattia Bernetti, Alisha Jones +2
Chemical probing experiments such as SHAPE are routinely used to probe RNA molecules. In this work, we use atomistic molecular dynamics simulations to test the hypothesis that bind…
Towards empirical force fields that match experimental observables
Thorben Fröhlking, Mattia Bernetti, Nicola Calonaci +1
Biomolecular force fields have been traditionally derived based on a mixture of reference quantum chemistry data and experimental information obtained on small fragments. However,…
Machine learning a model for RNA structure prediction
Nicola Calonaci, Alisha Jones, Francesca Cuturello +2
RNA function crucially depends on its structure. Thermodynamic models currently used for secondary structure prediction rely on computing the partition function of folding ensemble…