SHAPER: 3D Structure-SHAPE predictoR


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Note: The names of files to be uploaded should only contain alphanumeric characters, period (.), hypen (-), and underscore (_).

3D RNA pdb file: Input 3D RNA structure file should be in PDB format.
File should only contain RNA structure with size < 10 MB.
If file contains multiple models,
predicted SHAPE profile for each model will be provided.
The residue number will be renumbered.

SHAPE txt file (optional): SHAPE profile provided by user with size < 10 MB.
SHAPE reactivities should be in single column.

MASK txt file (optional): MASK file provided by user with size < 10 MB.
Mask values should be in single column,
with 0 and 1 for unmasked and masked residue, respectively.
Default mask values are 0s for all residues.

Your email address (optional): You will receive the results by email, if provided.

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References

SHAPER: Used to predict SHAPE reactivity from 3D structure with sequence-dependent bias. 3DSSR: Used to predict SHAPE reactivity from 3D structure. DSSR: Used to extract 2D structure. RNAView: Used to identify base pair types. VMD: Used to calculate solvent accessibility.