74 citations · 112 across the 3 of their papers we have counts for
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q-bio.BM2022★ 6 cited
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…
q-bio.BM2020★ 32 cited
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…