Mfold web server for nucleic acid folding and hybridization prediction

By M. Zuker. Nucleic Acids Res., 2003

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Citations in the corpus

Diversity, Activity, and Evolution of CRISPR Loci in Streptococcus thermophilus (2007, methodology): “thermophilus CRISPR repeats by using the Mfold program (26), as shown in Fig.”
Plant microRNA: a small regulatory molecule with big impact. (2006, background): “, 2004b) as predicted by MFOLD (Zuker, 2003; Mathews et al., 1999) or other computational programs.”
A practical approach to RT-qPCR-Publishing data that conform to the MIQE guidelines. (2010, methodology): “The program MFOLD (http://unafold.rna.albany.edu/?q=mfold/dna-folding-form) can then be used to analyze the amplicon for potential secondary structures that may prevent efficient amplification (Zuker 2003) (Figure 2).”
Analysis of Thermal Melting Curves (2003, neutral): “( Zuker, 1989, 2003; It is possible to form double-stranded structures that do not resemble classic B-DNA by twisting and turning the nucleic acid.”
Taxonomic reassessment of the genus Chlorella (Trebouxiophyceae) using molecular signatures (barcodes), including description of seven new species. (2011, methodology): “To locate hemi–compensatory base changes (hemi–CBCs) and CBCs, the ITS–2 secondary structure was constructed with the help of mfold (zuker 2003) and 4SALE (seiBel et al.”
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. (2009, methodology): “secondary structure is available through tools such as the thermodynamic method, Mfold (Zuker 2003), and the probabilistic method, Contrafold (Do et al.”
Duplex unwinding and ATPase activities of the DEAD-box helicase eIF4A are coupled by eIF4G and eIF4B (2011, methodology): “The stability of individual duplex regions is determined by the nearest-neighbor method, which involves the connection of the duplex strands by a tetraloop sequence for computation purposes.(46) The absence of a tetraloop connecting the duplexes in our experiments is accounted for by the addition of”
Thermodynamics of RNA-RNA Binding (2006, methodology): “A restricted variant of this approach is implemented in the program RNAhybrid [29], see also [41, 4]: here secondary structures within both monomers are neglected so that only intermolecular base pairs are taken into account.”
RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. (2005, methodology): “Ever since the emergence of mfold (multiple folds) it has been a common practice to report a number of suboptimal folds for predicitive purposes (Zuker 1989, 2003).”
Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts (2014, neutral): “35); (13) UAAC tetraloop (PDB: 4A4R36); (14) UCAC tetraloop (PDB: 4A4S36); (15) UGAC tetraloop (PDB: 4A4U36); (16) UUAC tetraloop (PDB: 4A4T36); (17) chimp HAR1 GAA loop (PDB: 2LHP37); (18) human HAR1 GAA loop (PDB: 2LUB37); (19) GU:UAU internal loop (unpublished data; M.”
Conservation and divergence of plant microRNA genes. (2006, background): “1 (Mathews et al., 1999; Zuker, 2003) that is publicly available at http://www.”
Revision of the Synechococcales (Cyanobacteria) through recognition of four families including Oculatellaceae fam. nov. and Trichocoleaceae fam. nov. and six new genera containing 14 species (2018, methodology): “…(ITS) were not aligned, but secondary structures including D1-D1’, Box B, V2 and V3 helices were identified and predicted using the Mfold web server (Zuker 2003). additional conserved domains (all helices plus D2, D3, Box a, D4, and D5) were identified for comparison of lengths. all structures…”
SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands. (2007, methodology): “This program of Zuker (2003) calculates the possible configuration of single-stranded nucleic acids by energy minimizing method considering stems, loops and bulges.”
Dynamic DNA nanotechnology using strand-displacement reactions. (2011, background): “[104] Zuker, M.”
Molecular phylogenetics of Braconidae (Hymenoptera: Ichneumonoidea), based on multiple nuclear genes, and implications for classification (2011, methodology): “A model was also determined for the D1 expansion region of 28S rDNA using the Mfold web server (Zuker, 2003) and the methods outlined in Gillespie (2004).”
Morphological and molecular characterization of selected desert soil cyanobacteria: three species new to science including Mojavia pulchra gen. et sp. Nov. (2007, methodology): “Secondary structures of conserved regions of the 16S-23S rRNA ITS regions were determined using RNA Mfold version 2.3 (Zuker 2003), with folding temperature set at 20uC.”