HiRE-RNA is a simplified, coarse-grained model, developed in recent years to address the question of RNA folding for the prediction of equilibrium configurations, dynamics and thermodynamics. Earlier versions of the model predicted simple folds such as hairpins and double helices. Important modifications in the force field now allow us to treat a much larger variety of structures thanks to the possibility of one base to form multiple contacts and non-canonical pairings, which are essential for the formation and the stability of structures such as pseudoknots, multiple helices, and the complex architecturesof riboswitches\mus  .
HiRE-RNA is a simplified, coarse-grained RNA model for the prediction of equilibrium configurations, dynamics and thermodynamics. Using a reduced set of particles and detailed interactions accounting for base-pairing and stacking we show that non-canonical and multiple base interactions are necessary to capture the full physical behavior of complex RNAs. In this paper we give a full account of the model and we present results on the folding, stability and free energy surfaces of 16 systems with 12 to 76 nucleotides of increasingly complex architectures, ranging from monomers to dimers, using a total of 850\mus simulation time .
R
model, developed in recent years to address the question of RNA folding
RNA model
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Earlier versions of the model predicted simple folds such as hairpins and double helices. Important modifications in the force field now allow us to treat a much larger variety of structures thanks to the possibility of one base to form multiple contacts and
Using a reduced set of particles and detailed interactions accounting for base-pairing and stacking we show that
R
pairings, which are essential for the formation and the stability of structures such as pseudoknots, multiple helices, and the complex architecturesof riboswitches
and multiple base interactions are necessary to capture the full physical behavior of complex RNAs. In this paper we give a full account of the model and we present results on the folding, stability and free energy surfaces of 16 systems with 12 to 76 nucleotides of increasingly complex architectures, ranging from monomers to dimers, using a total of 850
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simulation time