TiRNA: a coarse-grained method with temperature and ion effects for RNA structure folding and prediction

RNAs play crucial roles in various important biological functions such as gene regulation and catalysis. The functions of RNAs are generally coupled to their structures as well as to the stability of the structure, which can strongly depend on ionic conditions. However, it is still a challenge to make reliable predictions for the structures and stability of RNAs in ion solutions. In this work, we developed a coarse-grained method involving temperature and ion effects for simulating RNA folding and three-dimensional (3D) structure prediction, named TiRNA. Extensive tests demonstrate that TiRNA can make successful predictions for 3D structures of RNAs, including pseudoknots and multi-way junctions, and for thermal stability of RNAs in ion solutions solely from sequences, as compared with the top existing methods. Moreover, TiRNA can also make reliable predictions for 3D structures and stability of RNAs in ion solutions based on inputting secondary structures.