IsRNA is a coarse-grained model for de novo prediction and blind screening of RNA 3D structures.
The model has three main features: a four/five-bead coarse-grained representation for pyrimidine/purine nucleotides, a coarse-grained force field extracted through rigorous reference state simulations, and replica-exchange molecular dynamics simulations for conformational sampling. The server contains the following two modules: (1) "Structure Prediction": To fold tertiary structures of large-size RNAs with complicated topologies with given secondary structure constraints; (2) "Structure Assessment": To select structure models from a pool of candidate conformations without prior knowledge of the native structure.
If experimental SHAPE data is available, our SHAPE web server allows users to exclude SHAPE-incompatible structures, and the results can be used to guide the 3D structure selection. Link to SHAPE web server
 Zhang D, Li J and Chen S-J. (2020) IsRNA1: de novo prediction and blind screening of RNA 3D structures.
 Zhang D and Chen S-J. (2018) IsRNA: An iterative simulated reference state approach to modeling correlated interactions in RNA folding. J. Chem. Theory Comput., 14, 2230-2239.