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.
One of the challenges in predicting RNA secondary structure is that standard free energy minimization and statistical sampling methods cannot identify pseudoknots. The primary issue lies in the usual dynamic programming algorithms, which only consider interactions between adjacent nucleotides when predicting structures, whereas pseudoknotted configurations arise from distant nucleotide interactions. Rivas and Eddy introduced a dynamic programming algorithm for pseudoknot prediction.