For calculations involving multiple strands:
- R.M. Dirks, J.S. Bois, J.M. Schaeffer, E. Winfree, and N.A. Pierce. (2007) Thermodynamic analysis of interacting nucleic acid strands. SIAM Rev, 49, 65-88. (pdf)
For calculations involving pseudoknots:
- R.M. Dirks and N.A. Pierce. (2003) A partition function algorithm for nucleic acid secondary structure including pseudoknots. J Comput Chem, 24, 1664-1677. (pdf, supp info)
- R.M. Dirks and N.A. Pierce. (2004) An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. J Comput Chem, 25, 1295-1304. (pdf)