pknotsRG is a tool for folding RNA secondary structures, including the class of simple recursive pseudoknots. The program runs in O(n^4) time and O(n^2) space, therefore its application here on the BiBiserv is limited to sequences of length up to 600 bases. The energy parameters for structures containing no pseudoknots are the same as in the actual mfold 3.1. The energy for pseudoknots is computed with a model similar to that used by Rivas&Eddy in pknotsRE. The folding temperature is fixed to 37C.
