catRAPID RNA modifications
catRAPID RNA modifications is a dedicated webserver that can incorparate changes in the RNA strucutre caused by RNA modifications and estimate the impact of those in the interaction propensity against a protein set of interest.
Using the Vienna algorithm, we are now able to incorporate changes in the RNA structure caused by inosine (I), pseudouridine (P), dihydrouridine (D), m6A (6), 7DA (7), and nebularine (9). The user should use I, P, D, 6, 7, and 9 corresponding to the modified nucleotide. The predictions of catRAPID are then run with the modified nucleotide. The server will automatically compute differences in interaction propensities between the modified and unmodified nucleotide, providing:
- ΔΔG: The difference in RNA energy due to the modification.
- ΔI: The difference in interaction propensity between the modified and unmodified states (ΔI = Ix - Iy).
Since catRAPID is using an ensemble of RNA structures in its calculations, and the presence of the modification can alter the ranking of these structures, then the final score in catRAPID calculations might be influenced.
For details about this version of catRAPID, please refer to this documentation.