The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.
UNAFold
Abstract
The UNAFold software package is an integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. The name is derived from "Unified Nucleic Acid Folding." Folding (secondary structure) prediction for single-stranded RNA or DNA combines free energy minimization, partition function calculations and stochastic sampling. For melting simulations, the package computes entire melting profiles, not just melting temperatures. UV absorbance at 260 nm, heat capacity change (C(p)), and mole fractions of different molecular species are computed as a function of temperature. The package installs and runs on all Unix and Linux platforms that we have looked at, including Mac OS X. Images of secondary structures, hybridizations, and dot plots may be computed using common formats. Similarly, a variety of melting profile plots is created when appropriate. These latter plots include experimental results if they are provided. The package is "command line" driven. Underlying compiled programs may be used individually, or in special combinations through the use of a variety of Perl scripts. Users are encouraged to create their own scripts to supplement what comes with the package. This evolving software is available for download at http://www.bioinfo.rpi.edu/applications/hybrid/download.php .
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Citations
Cites
Bellman, R. E. (2010) · doi:10.1515/9781400835386 · Cited by 14,588
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-citationMolecular Beacons: Probes that Fluoresce upon Hybridization
Tyagi, S., & Kramer, F. R. (1996) · Nature Biotechnology · doi:10.1038/nbt0396-303 · Cited by 4,155
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-citationOptimal computer folding of large RNA sequences using thermodynamics and auxiliary information
Zuker, M., & Stiegler, P. (1981) · Nucleic Acids Research · doi:10.1093/nar/9.1.133 · Cited by 3,562
Self-citationA unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
SantaLucia, J. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.4.1460 · Cited by 2,793
Vienna RNA secondary structure server
Hofacker, I. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg599 · Cited by 2,345
Fast folding and comparison of RNA secondary structures
Hofacker, I. L., Fontana, W., Stadler, P. F., Bonhoeffer, L. S., Tacker, M., & Schuster, P. (1994) · Monatshefte f�r Chemie Chemical Monthly · doi:10.1007/bf00818163 · Cited by 2,306
Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison
Sankoff, D., & Kruskal, J. B. (1983) · Medical Entomology and Zoology · Cited by 1,915
The 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
Cited by
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
Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding
Helwak, A., Kudla, G., Dudnakova, T., & Tollervey, D. (2013) · Cell · doi:10.1016/j.cell.2013.03.043 · Cited by 1,269
The RNA modification database, RNAMDB: 2011 update
Cantara, W. A., Crain, P. F., Rozenski, J., McCloskey, J. A., Harris, K. A., Zhang, X., Vendeix, F. A. P., Fabris, D., & Agris, P. F. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1028 · Cited by 820
Automated model building and protein identification in cryo-EM maps
Jamali, K., Käll, L., Zhang, R., Brown, A., Kimanius, D., & Scheres, S. H. W. (2023) · doi:10.1101/2023.05.16.541002 · Cited by 686
Automated model building and protein identification in cryo-EM maps
Jamali, K., Käll, L., Zhang, R., Brown, A., Kimanius, D., & Scheres, S. H. W. (2024) · Nature · doi:10.1038/s41586-024-07215-4 · Cited by 686
Metadata
- Authors
- Markham, N. R., & Zuker, M.
- Venue
- Methods in Molecular Biology™
- Publisher
- Humana Press
- Published
- 2008
- Volume
- 453
- Pages
- 3-31
- ISSN
- 1064-3745 (ISSN-L)
- OpenAlex
- W2400250419
- Cited by
- 1,018
- References
- 31
- FWCI
- 58.25
- Type
- book chapter
- Language
- en
- Open access
- closed
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
