Single sequence prediction methods are always limited by the underlying RNA folding model. This may be the set of free energy parameters used by free energy minimization methods or the underlying methodological framework such as maximum expected accuracy methods. DotKnot-PW shows excellent results on H-type pseudoknots with short interhelix loops. For this type of pseudoknots, DotKnot-PW uses free energy pseudoknot parameters by Chen (2006, 2009 ) based on polymer statistical mechanics. Improvements of the accuracy of free energy parameters, both for secondary structures and pseudoknots, will lead to more accurate prediction methods. However, one has to keep in mind that the algorithms themselves must be designed in such a fashion that novel parameters can be efficiently incorporated. The heuristic framework of DotKnot-PW has been designed such that it can incorporate sophisticated free energy parameters for pseudoknots, secondary structures and coaxial stacking. In the future, DotKnot-PW could also use contributions from basic tertiary structure elements such as base triples around the pseudoknot junction or stem-loop interactions.