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 an 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, or structures with missing atoms, we recommend submitting complete, single-stranded structures 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.
|References for SHAPER:|
|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.|