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

TL;DR

This paper introduces HiRE-RNA, a coarse-grained model capable of predicting RNA folding pathways, free energy surfaces, and complex structures, validated on various RNA systems with extensive simulations.

Contribution

The paper presents a detailed coarse-grained RNA model that incorporates non-canonical interactions for accurate structure and thermodynamics prediction.

Findings

Successfully modeled folding and stability of diverse RNA structures.

Captured complex interactions necessary for realistic RNA behavior.

Performed extensive simulations totaling 850 microseconds.

Abstract

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$\mu$s simulation time.