NUPACK: Analysis and design of nucleic acid systems
Open accessAbstract
The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server ( http://www.nupack.org ) currently enables: Analysis: thermodynamic analysis of dilute solutions of interacting nucleic acid strands. Design: sequence design for complexes of nucleic acid strands intended to adopt a target secondary structure at equilibrium. Utilities: evaluation, display, and annotation of equilibrium properties of a complex of nucleic acid strands. NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The paper's data captured and quantitated the repressive effect of secondary structure on ribosome load.
“By calculating UTR minimum free energies (MFE)26 and comparing them to UTR MRLs, we captured and quantitated this repressive effect of secondary structure on ribosome load (Supplementary Fig. 2c)17,25.”
From Human 5′ UTR design and variant effect prediction from a massively parallel translation assay (2019) · cites this paper as [26]
Cited by
Sorted by citations
Lorenz, R., Bernhart, S. H., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P. F., & Hofacker, I. L. (2011) · Algorithms for Molecular Biology · doi:10.1186/1748-7188-6-26 · Cited by 5,098 · see citing works
Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds
Zalatan, J. G., Lee, M. E., Almeida, R., Gilbert, L. A., Whitehead, E. H., La Russa, M., Tsai, J. C., Weissman, J. S., Dueber, J. E., Qi, L. S., et al. (2015) · Cell · doi:10.1016/j.cell.2014.11.052 · Cited by 938 · see citing works
Random access in large-scale DNA data storage
Organick, L., Ang, S. D., Chen, Y.-J., Lopez, R., Yekhanin, S., Makarychev, K., Racz, M. Z., Kamath, G., Gopalan, P., Nguyen, B., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4079 · Cited by 775 · see citing works
Causes and effects of N-terminal codon bias in bacterial genes
Goodman, D. B., Church, G. M., & Kosuri, S. (2013) · Science · doi:10.1126/science.1241934 · Cited by 573 · see citing works
Highly multiplexed <i>in situ</i> protein imaging with signal amplification by Immuno-SABER
Saka, S. K., Wang, Y., Kishi, J. Y., Zhu, A., Zeng, Y., Xie, W., Kirli, K., Yapp, C., Cicconet, M., Beliveau, B. J., et al. (2018) · doi:10.1101/507566 · Cited by 485 · see citing works
Human 5′ UTR design and variant effect prediction from a massively parallel translation assay
Sample, P. J., Wang, B., Reid, D. W., Presnyak, V., McFadyen, I. J., Morris, D. R., & Seelig, G. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0164-5 · Cited by 442 · see citing works
Advancement of the emerging field of RNA nanotechnology
Jasinski, D., Haque, F., Binzel, D. W., & Guo, P. (2017) · ACS Nano · doi:10.1021/acsnano.6b05737 · Cited by 352 · see citing works
Diverse and robust molecular algorithms using reprogrammable DNA self-assembly
Woods, D., Doty, D., Myhrvold, C., Hui, J., Zhou, F., Yin, P., & Winfree, E. (2019) · Nature · doi:10.1038/s41586-019-1014-9 · Cited by 295 · see citing works
Theoretical basis for stabilizing messenger RNA through secondary structure design
Wayment-Steele, H. K., Kim, D. S., Choe, C. A., Nicol, J. J., Wellington-Oguri, R., Watkins, A. M., Parra Sperberg, R. A., Huang, P.-S., Participants, E., & Das, R. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab764 · Cited by 197 · see citing works
DNA assembly for nanopore data storage readout
Lopez, R., Chen, Y.-J., Dumas Ang, S., Yekhanin, S., Makarychev, K., Racz, M. Z., Seelig, G., Strauss, K., & Ceze, L. (2019) · Nature Communications · doi:10.1038/s41467-019-10978-4 · Cited by 142 · see citing works
Driving the Scalability of DNA-Based Information Storage Systems
Tomek, K. J., Volkel, K., Simpson, A., Hass, A. G., Indermaur, E. W., Tuck, J. M., & Keung, A. J. (2019) · ACS Synthetic Biology · doi:10.1021/acssynbio.9b00100 · Cited by 100 · see citing works
Su, H., Xu, J., Wang, Q., Wang, F., & Zhou, X. (2019) · Nature Communications · doi:10.1038/s41467-019-13310-2 · Cited by 94 · see citing works
Alexaki, A., Hettiarachchi, G. K., Athey, J. C., Katneni, U. K., Simhadri, V., Hamasaki-Katagiri, N., Nanavaty, P., Lin, B., Takeda, K., Freedberg, D., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-51984-2 · Cited by 78 · see citing works
Nucleic Acid Databases and Molecular-Scale Computing
Song, X., & Reif, J. (2019) · ACS Nano · doi:10.1021/acsnano.9b02562 · Cited by 73 · see citing works
DNA Data Storage and Hybrid Molecular–Electronic Computing
Carmean, D., Ceze, L., Seelig, G., Stewart, K., Strauss, K., & Willsey, M. (2019) · Proceedings of the IEEE · doi:10.1109/jproc.2018.2875386 · Cited by 69 · see citing works
Characterization and Repurposing of Type I and Type II CRISPR–Cas Systems in Bacteria
Hidalgo-Cantabrana, C., Goh, Y. J., & Barrangou, R. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.09.013 · Cited by 63 · see citing works
A Mixed Culture of Bacterial Cells Enables an Economic DNA Storage on a Large Scale
Hao, M., Qiao, H., Gao, Y., Wang, Z., Qiao, X., Chen, X., & Qi, H. (2020) · Communications Biology · doi:10.1038/s42003-020-01141-7 · Cited by 41 · see citing works
Reprogramming eukaryotic translation with ligand-responsive synthetic RNA switches
Anzalone, A. V., Lin, A. J., Zairis, S., Rabadan, R., & Cornish, V. W. (2016) · Nature Methods · doi:10.1038/nmeth.3807 · Cited by 33 · see citing works
Metastable hybridization-based DNA information storage to allow rapid and permanent erasure
Kim, J., Bae, J. H., Baym, M., & Zhang, D. Y. (2020) · Nature Communications · doi:10.1038/s41467-020-18842-6 · Cited by 29 · see citing works
Assessment of Nucleic Acid Structure Prediction in <scp>CASP16</scp>
Kretsch, R. C., Hummer, A. M., He, S., Yuan, R., Zhang, J., Karagianes, T., Cong, Q., Kryshtafovych, A., & Das, R. (2026) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.70072 · Cited by 51 · see citing works
“Knotty (last commit March 28, 2018) [57], NUPACK (3.0.6) [58, 59] and pknots (last commit January 30, 2020) [60] were all run with the pseudo-knot option on.”
InfluentialEngineered retrons generate genome-independent protein-binding DNA for cellular control
Lee, G., & Kim, J. (2023) · doi:10.1101/2023.09.27.556556 · Cited by 15 · see citing works
CRISPRmap: Sequencing-free optical pooled screens mapping multi-omic phenotypes in cells and tissue
Gu, J., Iyer, A., Wesley, B., Taglialatela, A., Leuzzi, G., Hangai, S., Decker, A., Gu, R., Klickstein, N., Shuai, Y., et al. (2023) · doi:10.1101/2023.12.26.572587 · Cited by 10 · see citing works
Venero, O. M., Ndeh, R., Pan, A., Patrikainen, P., Eriksson, M., Akhgari, A., Kakko, L., Nedorezova, D., Mohamed, O., Thomson, L., et al. (2026) · BMC Biotechnology · doi:10.1186/s12896-025-01098-7 · Cited by 3 · see citing works
- Authors
- Zadeh, J. N., Steenberg, C. D., Bois, J. S., Wolfe, B. R., Pierce, M. B., Khan, A. R., Dirks, R. M., & Pierce, N. A.
- Affiliations
- California Institute of Technology (US)
- Corresponding author
- Pierce, Niles A.
- Venue
- Journal of Computational Chemistry
- Publisher
- Wiley
- Published
- 2010-11-17
- Volume
- 32
- Issue
- 1
- Pages
- 170-173
- ISSN
- 0192-8651 (ISSN-L)
- 1096-987X
- OpenAlex
- W1989020100
- Cited by
- 1,670
- References
- 0
- Citations by year
- 2026: 157 · 2025: 177 · 2024: 150 · 2023: 175 · 2022: 151 · 2021: 150 · 2020: 110 · 2019: 120 · 2018: 121 · 2017: 87 · 2016: 65 · 2015: 61 · 2014: 57 · 2013: 25 · 2012: 44
- FWCI
- 10.44
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Journal of Computational Chemistry (publishedVersion)
- PubMed (publishedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Funders
- National Human Genome Research Institute (P50HG004071)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- nucleic acid secondary structure, thermodynamic analysis, sequence design, nucleic acid complexes, pseudoknot, web server, structural ensembles
- MeSH terms
- DNA, Models, Molecular, Nucleic Acid Conformation, Nucleic Acids, RNA, Software
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
