One of the issues when predicting RNA secondary structure is that the standard free energy minimization and statistical sampling methods can not find pseudoknots. The major problem is that the usual dynamic programing algorithms, when predicting secondary structure, consider only the interactions between the closest nucleotides, while pseudoknotted structures are formed due to interactions between distant nucleotides. Rivas and Eddy published a dynamic programming algorithm for predicting pseudoknots.
A challenge in RNA secondary structure prediction is that standard methods cannot identify pseudoknots. The main issue arises from usual dynamic programming algorithms, which only consider nearby interactions when predicting structures, whereas pseudoknotted arrangements are formed by distant nucleotide connections. Rivas and Eddy introduced a dynamic programming algorithm for pseudoknot detection.