C-RCPred: Constrained RNA Complex Prediction
C-RCPred is a multi-objective tool for secondary structure prediction of RNA complexes taking into account constraints (base pairs, single bases, helices, loops, pseudoknots) and probing data (SHAPE, PARS, DMS).
C-RCPred handle the prediction of pseudoknots and of crossing interactions.
It returns several sub-optimal secondary structures.
It takes as inputs several possible secondary structures for each RNA strand involved in the complex and several possible interactions for each pair of RNAs.
C-RCPred is based on a constrained maximum weight clique graph problem. The principal idea is to find the best combinations of the inputs forming cliques that can be derived into secondary structures of a complex.