NUPACK Web Application
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M. E. Fornace, J. Huang, C. T. Newman, N. J. Porubsky, M. B. Pierce,
N. A. Pierce. NUPACK: analysis and design of nucleic acid structures, devices, and systems.
ChemRxiv, 2022.
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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 Python Module
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M. E. Fornace, J. Huang, C. T. Newman, N. J. Porubsky, M. B. Pierce,
N. A. Pierce. NUPACK: analysis and design of nucleic acid structures, devices, and systems.
ChemRxiv, 2022.
NUPACK Analysis Algorithms
- M. E. Fornace, N. J. Porubsky, and N. A. Pierce. 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)
- 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)
NUPACK Design Algorithms
- B. R. Wolfe, N. J. Porubsky, J. N. Zadeh, R. M. Dirks, and N. A. Pierce.
Constrained multistate sequence design for nucleic acid reaction pathway engineering. J Am Chem Soc, 139:3134-3144, 2017.
(pdf,
supp info)
- B. R. Wolfe and N. A. Pierce. Sequence design for a test tube of
interacting nucleic acid strands.
ACS Synth Biol, 4:1086-1100, 2015.
(pdf,
supp info,
supp tests)
- J. N. Zadeh, B. R. Wolfe, and N. A. Pierce. Nucleic acid sequence
design via efficient ensemble defect optimization.
J Comput Chem, 32:439–452, 2011.
(pdf,
supp info,
supp tests)
- R. M. Dirks, M. Lin, E. Winfree, and N. A. Pierce. Paradigms for
computational nucleic acid design.
Nucl Acids Res, 32:1392-1403, 2004.
(pdf,
supp info,
supp seqs)
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