The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Sfold web server for statistical folding and rational design of nucleic acids
Open accessAbstract
The Sfold web server provides user-friendly access to Sfold, a recently developed nucleic acid folding software package, via the World Wide Web (WWW). The software is based on a new statistical sampling paradigm for the prediction of RNA secondary structure. One of the main objectives of this software is to offer computational tools for the rational design of RNA-targeting nucleic acids, which include small interfering RNAs (siRNAs), antisense oligonucleotides and trans-cleaving ribozymes for gene knock-down studies. The methodology for siRNA design is based on a combination of RNA target accessibility prediction, siRNA duplex thermodynamic properties and empirical design rules. Our approach to target accessibility evaluation is an original extension of the underlying RNA folding algorithm to account for the likely existence of a population of structures for the target mRNA. In addition to the application modules Sirna, Soligo and Sribo for siRNAs, antisense oligos and ribozymes, respectively, the module Srna offers comprehensive features for statistical representation of sampled structures. Detailed output in both graphical and text formats is available for all modules. The Sfold server is available at http://sfold.wadsworth.org and http://www.bioinfo.rpi.edu/applications/sfold.
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Cites
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
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
Rational siRNA design for RNA interference
Reynolds, A., Leake, D., Boese, Q., Scaringe, S., Marshall, W. S., & Khvorova, A. (2004) · Nature Biotechnology · doi:10.1038/nbt936 · Cited by 2,094
Xia, T., SantaLucia, J., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X., Cox, C., & Turner, D. H. (1998) · Biochemistry · doi:10.1021/bi9809425 · Cited by 1,140
Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes
Sugimoto, N., Nakano, S.-I., Katoh, M., Matsumura, A., Nakamuta, H., Ohmichi, T., Yoneyama, M., & Sasaki, M. (1995) · Biochemistry · doi:10.1021/bi00035a029 · Cited by 697 · cited 1×
“The antisense oligo binding energy is a weighted sum of the DNA/RNA stacking energies (21) for the hybrid formed by the antisense oligo and the targeted sequence.”
BackgroundEfficient Reduction of Target RNAs by Small Interfering RNA and RNase H-dependent Antisense Agents
Vickers, T. A., Koo, S., Bennett, C. F., Crooke, S. T., Dean, N. M., & Baker, B. F. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m210326200 · Cited by 461
Cited by
VARNA: Interactive drawing and editing of the RNA secondary structure
Darty, K., Denise, A., & Ponty, Y. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp250 · Cited by 1,356
MicroRNAs in Development and Disease
Sayed, D., & Abdellatif, M. (2011) · Physiological Reviews · doi:10.1152/physrev.00006.2010 · Cited by 1,078
Markham, N. R., & Zuker, M. (2008) · Methods in Molecular Biology™ · doi:10.1007/978-1-60327-429-6_1 · Cited by 1,018
Analyzing MiRNA–LncRNA Interactions
Paraskevopoulou, M. D., & Hatzigeorgiou, A. G. (2016) · Methods in Molecular Biology · doi:10.1007/978-1-4939-3378-5_21 · Cited by 895
Moitra, P., Alafeef, M., Dighe, K., Frieman, M. B., & Pan, D. (2020) · ACS Nano · doi:10.1021/acsnano.0c03822 · Cited by 745
Metadata
- Authors
- Ding, Y., Chan, C. Y., & Lawrence, C. E.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-07-01
- Volume
- 32
- Issue
- Web Server
- Pages
- W135-W141
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2133876293
- Cited by
- 518
- References
- 6
- FWCI
- 9.18
- Type
- journal article
- Language
- en
- Open access
- hybrid
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