NUPACK web server
- J.N. Zadeh, C.D. Steenberg, J.S. Bois, B.R. Wolfe, M.B. Pierce, A.R. Khan, R.M. Dirks, N.A. Pierce. NUPACK: analysis and design of nucleic acid systems. J Comput Chem, 32, 170–173, 2011. (pdf)
NUPACK analysis algorithms
- 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)
- 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)
NUPACK design algorithms
- J.N. Zadeh, B.R. Wolfe, N.A. Pierce. Nucleic acid sequence design via efficient ensemble defect optimization. J Comput Chem, 32, 439–452, 2011. (pdf, supp info, supp tests)