188 citations · 834 across the 13 of their papers we have counts for
10 papers · 1 filter
A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs
Simón Poblete, Sandro Bottaro, Giovanni Bussi
We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained representation of RNA designed for structure prediction and refinement. In our approach, the representation of a n…
Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies
Petra Kührová, Robert B. Best, Sandro Bottaro +4
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motif…
Free Energy Landscape of GAGA and UUCG RNA Tetraloops
Sandro Bottaro, Pavel Banáš, Jiri Sponer +1
We report the folding thermodynamics of ccUUCGgg and ccGAGAgg RNA tetraloops using atomistic molecular dynamics simulations. We obtain a previously unreported estimation of the fol…
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…
Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments
Giovanni Pinamonti, Sandro Bottaro, Cristian Micheletti +1
Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. Th…