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Pseudoknot


A pseudoknot is an RNA secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982. Pseudoknots fold into...
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Most information from pseudoknot is available on this portal. This portal also allows for automatic visualization of pseudoknot structures using Pseudoviewer. ...
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Most ab initio pseudoknot predicting methods provide very few folding scenarios ... In this study, we introduce the Pseudoknot Local Motif Model and Dynamic Partner ...
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This structure has a "pseudoknot," indicated by the presence of crossed arcs in ... Of the 43 sequences, 11 are pseudoknot-free (namely the tRNA sequences and five ...
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conformational loops that we call pseudoknot core units, using the theory of ... We also find that the entropy of a pseudoknot loop depends not only on its ...
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the beet western yellows virus pseudoknot reveals strongly pH-depen ... speci®c interactions that a pseudoknot can form, as ... BWYV pseudoknot structure as ...
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type RNA pseudoknot, optimally positioned six to eight ... pairing, and potential stacking of pseudoknot helical stems, ... BWYV pseudoknot reveals significant ...
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RNA pseudoknot structure is defined as a ... A simple pseudoknot is composed of two helix ... logical functions of a pseudoknot are directly related to the ...
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... looped strand of RNA that forms what is called a "pseudoknot," was revealed ... retroviruses by binding to the pseudoknot at this site and blocking these ...
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... Rfam alignment (UPSK RNA) with a pseudoknot in Stockholm format is shown below: ... characters from the English alphabet indicate pseudoknot interactions. ...
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... work has suggested that the pseudoknot is part of a tRNA ... ( C) Pseudoknot mutations used ... that form the proposed pseudoknot interactions (regions 1 and 2) ...
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For pseudoknot-free structures, ncRNA search can be effective based on the ... perform fast yet accurate RNA pseudoknot searches, we need novel heuristics to ...
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The structure of this pseudoknot is unusual. ... The 3D-modeling of pseudoknot topologies shows that such loops do not cross any ...
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( B) The nucleotide sequence of the RNA pseudoknot co-crystallized with RT. ... Figure 2 Electron density maps of HIV-1 RT complexed with the RNA pseudoknot. ...
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The role of the pseudoknot in the TLS of plant viral RNAs is quite puzzling. On one hand, the pseudoknot as a central part of the TLS is required for ...
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The pseudoknot is preceded by a conserved slippery heptanucleotide (Y CCU UUU) ... Positioned 5' of the pseudoknot, and separated from it by a 5 nt spacer, is a ...
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Pseudoknot elements in human and the budding yeast Kluyveromyces lactis ... We analyzed the pseudoknot sequences in 28 ciliate species ... Pseudoknot junctions ...
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