Sfold web server for statistical folding and rational design of nucleic acids

By Ye Ding, Chi Yu Chan, Charles E. Lawrence. Nucleic Acids Res., 2004

535 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e086e706dadda03a003e89983a922b8af463b9d9

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Citations in the corpus

A structural analysis of in vitro catalytic activities of hammerhead ribozymes (2007, unknown): “The structure sampling method has been implemented in the Sfold software program for RNA folding and applications [33] and is used here for mRNA folding.”
The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse (2013, methodology): “The red curve shows the average probability of single-stranded RNA (Ding et al., 2004).”
NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure (2009, background): “Such programs include Mfold/UnaFold (8,9), the Vienna RNA package (10), RNA structure (2), RNAsoft (11) and Sfold (12).”
Thermodynamics of RNA-RNA Binding (2006, methodology): “The program Sfold [6, 5] adds a stochastic backtracking procedure to McCaskill’s partition function calculation [22] to generate a properly weighted sample of structures.”
On the art of identifying effective and specific siRNAs (2006, background): “A smaller number of algorithms consider the secondary structure and accessibility of the targeted mRN”