57 citations · 125 across the 3 of their papers we have counts for
3 papers
The mechanism of RNA base fraying: molecular dynamics simulations analyzed with core-set Markov state models
Giovanni Pinamonti, Fabian Paul, Frank Noé +2
The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and M…
Predicting the kinetics of RNA oligonucleotides using Markov state models
Giovanni Pinamonti, Jianbo Zhao, David E. Condon +4
Nowadays different experimental techniques, such as single molecule or relaxation experiments, can provide dynamic properties of biomolecular systems, but the amount of detail obta…
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…