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.

JobID:


Submit a new job for structure prediction:

(1) Job title (alphanumeric characters only):

(2) Input sequence (≤200 nucleotides) and 2D structure in dot-bracket format. Please use "-" to separate RNA strands for RNA complex systems (up to 10 strands)

(3) Initial 3D structures for simulations (optional; alphanumeric and underscore charaters only in the file names):

(4) Excluded templates (labeled by PDB ids) from database when generating initial 3D structures by Vfold3D/VfoldLA (optional):

(5) Simulation time (in nanosecond):

(6) Number of predicted structures:

(7) Number of recorded snapshots per replica:

(8) Fraction of the lowest-energy snapshots taken for clustering:

(9) RMSD cutoff for clustering (in Å):

(10) Your email address (optional, you will receive the results by email, if provided; !!!Note: Gmail could not receive email):

(11) Anti-robot:

Submit a new job for structure assessment:

(1) Job title (alphanumeric characters only):

(2) RNA sequence (please use "-" to separate RNA strands for RNA complex systems)

(3) Upload models (in PDB format; alphanumeric and underscore characters only in the file names):

(4) Simulation time (in nanosecond):

(5) Number of recorded snapshots per trajectory:

(6) Number of duplicate simulations per model:

(7) RMSD cutoff for collection of models' close decoys (in Å):

(8) Energy threshold to filter good models ≤ Emin

(9) Your email address (optional, you will receive the results by email, if provided; !!!Note: Gmail could not receive email):

(10) Anti-robot:


If experimental SHAPE data is available, our SHAPER web server allows users to exclude SHAPE-incompatible structures, and the results can be used to guide the 3D structure selection. Link to SHAPER web server
References
[1] Zhang D, Li J, Chen S-J. (2021) IsRNA1: de novo prediction and blind screening of RNA 3D structures. J. Chem. Theory Comput., 17(3):1842-57.
[2] 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.
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