188 citations · 834 across the 13 of their papers we have counts for
13 papers
How to learn from inconsistencies: Integrating molecular simulations with experimental data
Simone Orioli, Andreas Haahr Larsen, Sandro Bottaro +1
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly us…
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…
Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered Molecular Dynamics
Simón Poblete, Sandro Bottaro, Giovanni Bussi
Coarse-grained models can be of great help to address the problem of structure prediction in nucleic acids. On one hand they can make the prediction more efficient, while on the ot…
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…