The DOI matches its Crossref record.
Fast algorithm for predicting the secondary structure of single-stranded RNA.
Open accessAbstract
A computer method is presented for finding the most stable secondary structures in long single-stranded RNAs. It is 1-2 orders of magnitude faster than existing codes. The time required for its application increases as N3 for a chain N nucleotides long. As many as 1000 nucleotides can be searched in a single run. The approach is systematic and builds an optimal structure in a straightforward inductive procedure based on an exact mathematical algorithm. Two simple half-matrices are constructed and the best folded form is read directly from the second matrix by a simple back-tracking procedure. The program utilizes published values for base-pairing energies to compute one structure with the lowest free energy.
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Citations
Cited by
Mfold web server for nucleic acid folding and hybridization prediction
Zuker, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg595 · Cited by 13,404
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
Algorithm for Optimized mRNA Design Improves Stability and Immunogenicity
Zhang, H., Zhang, L., Lin, A., Xu, C., Li, Z., Liu, K., Liu, B., Ma, X., Zhao, F., Yao, W., et al. (2020) · arXiv · doi:10.48550/arxiv.2004.10177 · Cited by 511
Algorithm for optimized mRNA design improves stability and immunogenicity
Zhang, H., Zhang, L., Lin, A., Xu, C., Li, Z., Liu, K., Liu, B., Ma, X., Zhao, F., Jiang, H., et al. (2023) · Nature · doi:10.1038/s41586-023-06127-z · Cited by 531
RNA Pseudoknot Prediction in Energy-Based Models
Lyngsø, R. B., & Pedersen, C. N. S. (2000) · Journal of Computational Biology · doi:10.1089/106652700750050862 · Cited by 359
Metadata
- Authors
- Nussinov, R., & Jacobson, A. B.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 1980-11
- Volume
- 77
- Issue
- 11
- Pages
- 6309-6313
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2000191287
- Cited by
- 599
- References
- 0
- FWCI
- 1.74
- Type
- journal article
- Language
- en
- Open access
- green
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- Nussinov, R., & Jacobson, A. B. (1980). Fast algorithm for predicting the secondary structure of single-stranded RNA. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.77.11.6309
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