GU pairs are generally treated as nearest neighbor stacks, similar to Watson-Crick helices, and GU pairs at the ends of helices are penalized with the same parameter as AU pairs at the ends of helices. In one sequence context, a tandem GU pair with a GU followed by a UG, the nearest neighbor model does not work and two parameters are available, depending on the sequence context (see the html table of parameters). Note also that the motif 5'GG/3'UU is assigned a ∆G°37 of –0.5 kcal/mol to optimize structure prediction accurracy, whereas it is measured as +0.5 kcal/mol
A list of references is here.
A tutorial is available.