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HiRE-RNA is a simplified, coarse-grained RNA model for the prediction ofequilibrium configurations, dynamics and thermodynamics. Using a reduced set ofparticles and detailed interactions accounting for base-pairing and stacking weshow that non-canonical and multiple base interactions are necessary to capturethe full physical behavior of complex RNAs. In this paper we give a fullaccount of the model and we present results on the folding, stability and freeenergy surfaces of 16 systems with 12 to 76 nucleotides of increasingly complexarchitectures, ranging from monomers to dimers, using a total of 850$\mu$ssimulation time.

The coarse-grained HiRE-RNA model for de novo calculations of RNA free energy surfaces, folding pathways and complex structure prediction