NUPACK is a growing software suite for the analysis and design of nucleic acid structures, devices, and systems serving the needs of researchers in the fields of nucleic acid nanotechnology, molecular programming, synthetic biology, and across the life sciences more broadly.
Complex analysis and test tube analysis - M.E. Fornace, N.J. Porubsky, and N.A. Pierce (2020). A unified dynamic programming framework for the analysis of interacting nucleic acid strands: enhanced models, scalability, and speed. ACS Synth Biol , 9:2665-2678, 2020. ( pdf , supp info ) - R. M. Dirks, J. S. Bois, J. M. Schaeffer, E. Winfree, and N. A. Pierce. Thermodynamic analysis of interacting nucleic acid strands. SIAM Rev , 49:65-88, 2007. ( pdf ) Pseudoknot analysis - R. M. Dirks and N. A. Pierce. An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. J Comput Chem , 25:1295-1304, 2004. ( pdf ) - R. M. Dirks and N. A. Pierce. A partition function algorithm for nucleic acid secondary structure including pseudoknots. J Comput Chem , 24:1664-1677, 2003. ( pdf , supp info )
Latch Workflow Link - https://github.com/shivaramakrishna99/nupack-/ Acknowledgements - https://docs.nupack.org/#acknowledgments License - https://docs.nupack.org/#license