MODENA web server
Multi-objective design of RNA switches and structured RNA sequences. MODENA utilizes multi-objective optimization and RNA secondary structure prediction for computational RNA design.
Design templates
RNA-RNA interaction switch (RactIP)
This designs two RNA sequences that fold into a user-prescribed target JOINT structure. In addition, the user can specify target structures for single RNAs. An external pseudoknot (including a kissing-hairpin) is allowed (whereas pseudoknots within each sequence are not allowed).
RNA-RNA interaction switch (RNAcofold)
This designs two RNA sequences that fold into a user-prescribed target JOINT structure. In addition, the user can specify target structures for single RNAs. Any pseudoknotted joint secondary structure is not allowed.
Interacting two RNAs
This designs two RNA sequences that fold into a user-prescribed target JOINT secondary structure. An external pseudoknot is allowed (whereas pseudoknots within each sequence are not allowed)
Ligand-responsive RNA switch design
This designs a single RNA sequence that switches its secondary structure in response to ligand binding. An aptamer sequence and the secondary structure of its ligand-binding state have to be specified by user.
Inverse folding of a single RNA
This designs a single RNA sequence that folds into a user-prescribed target secondary structure.