SHAPER: 3D Structure-SHAPE predictoR

The SHAPER model provides user-friendly estimates of SHAPE reactivity from RNA 3D structures. The SHAPER model is an updated version of 3DSSR model, which takes RNA sequence-dependent bias into consideration. By analyzing structural features from a 3D RNA structure, such as 2D base-pairs, solvent accessibility of 2'-OH sites, stacking nucleotides, ribose sugar conformations, etc., the model can combine these key factors to predict the SHAPE reactivity for each nucleotide. By allowing users to exclude SHAPE-incompatible structures, results from this tool can be used to guide 3D structure prediction. If users also provide their SHAPE data, we will compute the correlation between the SHAPER-predicted profile and the user-provided experimental SHAPE reactivity.
Because the model was not parameterized using multistranded structures, broken structures, and structures with missing atoms, we recommend submitting complete, single-stranded clean structure to the server. Additionally, no structures with more than 174 nucleotides were used to parameterize the SHAPER model, so results from large RNA may not be valid.

Submit a new job

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.

Zhou Y, Li J, Hurst T, Chen S-J. (2021) SHAPER: A web server for fast and accurate SHAPE reactivity prediction. Frontiers in Molecular Biosciences, p.715.
Hurst T, Chen S-J. (2021) Sieving RNA 3D structures with SHAPE and Evaluating Mechanisms Driving Sequence-Dependent Reactivity Bias. The Journal of Physical Chemistry B, 125(4), 1156-1166.

3DSSR: Used to predict SHAPE reactivity from 3D structure.

Hurst T, Xu X, Zhao P, Chen S-J. (2018) Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis. The Journal of Physical Chemistry B, 122(18), 4771-4783.

DSSR: Used to extract 2D structure.

Lu X-J, Bussemaker H J, Olson W K. (2015) DSSR: an integrated software tool for dissecting the spatial structure of RNA. Nucleic Acids Research, 43(21):e142.

RNAView: Used to identify base pair types.

Yang H, Jossinet F, Leontis N, Chen L, Westbrook J, Berman H M, Westhof E. (2003) Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Research, 31(13):3450-3460.

VMD: Used to calculate solvent accessibility.

Humphrey W, Dalke A, Schulten K. (1996) VMD: visual molecular dynamics, Journal of Molecular Graphics, 14(1):33-38.

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