The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
On Finding All Suboptimal Foldings of an RNA Molecule
Abstract
An algorithm and a computer program have been prepared for determining RNA secondary structures within any prescribed increment of the computed global minimum free energy. The mathematical problem of determining how well defined a minimum energy folding is can now be solved. All predicted base pairs that can participate in suboptimal structures may be displayed and analyzed graphically. Representative suboptimal foldings are generated by selecting these base pairs one at a time and computing the best foldings that contain them. A distance criterion that ensures that no two structures are "too close" is used to avoid multiple generation of similar structures. Thermodynamic parameters, including free-energy increments for single-base stacking at the ends of helices and for terminal mismatched pairs in interior and hairpin loops, are incorporated into the underlying folding model of the above algorithm.
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Citations
Cites
Improved free-energy parameters for predictions of RNA duplex stability.
Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T., & Turner, D. H. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.24.9373 · Cited by 1,470
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
Self-citationThe C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
Lee, R. C., Feinbaum, R. L., & Ambros, V. (1993) · Cell · doi:10.1016/0092-8674(93)90529-y · Cited by 12,948
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
Mathews, D. H., Sabina, J., Zuker, M., & Turner, D. H. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2700 · Cited by 3,795
Self-citationThe Thermodynamics of DNA Structural Motifs
SantaLucia, J., & Hicks, D. (2004) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.32.110601.141800 · Cited by 1,314
Metadata
- Authors
- Zuker, M.
- Venue
- Science
- Published
- 1989-04-07
- Volume
- 244
- Issue
- 4900
- Pages
- 48-52
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2017313617
- Cited by
- 2,005
- References
- 1
- FWCI
- 16.24
- Type
- journal article
- Language
- en
- Open access
- closed
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- Zuker, M. (1989). On Finding All Suboptimal Foldings of an RNA Molecule. Science. https://doi.org/10.1126/science.2468181
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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