The MultiRNAFold package contains software for secondary structure prediction of one, two, or many interacting RNA or DNA molecules. It is composed of three pieces of software: SimFold, PairFold and MultiFold.
:: MORE INFORMATION
Mirela Andronescu, Zhi Chuan Zhang and Anne Condon,
“Secondary Structure Prediction of Interacting RNA Molecules“,
Journal of Molecular Biology, Vol 345/5 pp 987-1001.