UNAFold: software for nucleic acid folding and hybridization.

By Nicholas R. Markham, M. Zuker. Methods in molecular biology, 2008

1,014 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/12039cc5f13d4b3c2a04de3cd3cf0b10c4a9f87a

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Citations in the corpus

Noncoding RNA Gas5 Is a Growth Arrest and Starvation-Associated Repressor of the Glucocorticoid Receptor (2010, methodology): “We used the secondary-structure predictions from UNAFold (38) to guide tertiary structure predictions for the Gas5 RNA GRE-mimic and MRE-resembling region (39) (Fig.”
RNA secondary structure prediction using deep learning with thermodynamic integration (2020, methodology): “A number of tools including Mfold/UNAfold (4, 5), RNAfold (6, 7) and RNAstructure (8, 9) have adopted this approach.”
ViennaRNA Package 2.0 (2011, methodology): “Several other tools implement dynamic programming based RNA secondary structures prediction: UNAfold [19] is the successor of the original mfold program and adds suppport for predicting RNA-RNA hybridization.”
Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding (2013, neutral): “Sequences reliably mapped to two different sites were folded in silico using UNAFold (Markham and Zuker, 2008) to identify the interaction site of the RNA molecules that gave rise to the”
The ribosome binding site calculator. (2011, methodology): “This straightforward calculation may be carried out by the MFE program of NuPACK (Dirks et al., 2007), the RNAfold program of ViennaRNA (Gruber et al., 2008), or the hybrid-ss-min program of UNAFold (Markham and Zuker, 2008).”
RNA Secondary Structure Prediction By Learning Unrolled Algorithms (2020, methodology): “A few widely used methods such as RNAstructure (Bellaousov et al., 2013), Vienna RNAfold (Lorenz et al., 2011) and UNAFold (Markham & Zuker, 2008) (Bellaousov & Mathews, 2010) have been made to predict structures with pseudoknots, but the predictive accuracy and efﬁciency still need to be improved.”