In the following, a novel comparative approach for predicting structures including H-type pseudoknots called DotKnot-PW will be introduced. The input consists of two unaligned, evolutionarily related RNA sequences. Similarity scores between structure elements will be calculated. Statistically significant pairs will be used to find the set of conserved structure elements common to two sequences, which maximize a combined thermodynamic and similarity score. Using a hand-curated test set of pseudoknotted structures with experimental support, the prediction accuracy of DotKnot-PW will be compared with methods from the literature.