We have developed a method for predicting "guide strand of microRNAs
from its sequence and secondary structure" it is published in BMC
Bioinformatics see http://www.biomedcentral.com/1471-2105/10/105 .
Though it is developed to discriminate for guide and passenger strand
of miRNA but it can be used to design siRNA. I hope this information
will be useful for bioinformatics community.