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The Theory of Pseudoknots [PDF]
Journal of Knot Theory and Its Ramifications, 2012 Classical knots in $\mathbb{R}^3$ can be represented by diagrams in the plane. These diagrams are formed by curves with a finite number of transverse crossings, where each crossing is decorated to indicate which strand of the knot passes over at that ...
Henrich, Allison +5 more
core +2 more sources
PseudoknotVisualizer: Visualization of pseudoknots on three-dimensional RNA structures. [PDF]
PLoS Computational BiologyWe introduce the PseudoknotVisualizer, a specialized software designed to identify and visualize pseudoknots within RNA three-dimensional structures. Typically, RNA secondary structures containing pseudoknots can be decomposed into multiple pseudoknot ...
Takumi Otagaki +3 more
doaj +2 more sources
The 3' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin. [PDF]
PLoS ONE, 2012 The 3' splice site of influenza A segment 7 is used to produce mRNA for the M2 ion-channel protein, which is critical to the formation of viable influenza virions.
Walter N Moss +5 more
doaj +3 more sources
Nature Communications, 2021 Exoribonuclease-resistant RNAs (xrRNAs) are RNA elements that block the exoribonucleolytic degradation of RNA. Here the authors show how a long-range pseudoknot length modulates the Mg2+-dependence of flaviviral xrRNA’s folding, conformational dynamics ...
Xiaolin Niu +6 more
doaj +2 more sources
Hierarchical analysis of RNA secondary structures with pseudoknots based on sections. [PDF]
PLoS Computational BiologyPredicting RNA structures containing pseudoknots remains computationally challenging due to high processing costs and complexity. While standard methods for pseudoknot prediction require O(N6) time complexity, we present a hierarchical approach that ...
Ryota Masuki, Donn Liew, Ee Hou Yong
doaj +2 more sources
New models and algorithms for RNA pseudoknot order assignment
International Journal of Applied Mathematics and Computer Science, 2020 The pseudoknot is a specific motif of the RNA structure that highly influences the overall shape and stability of a molecule. It occurs when nucleotides of two disjoint single-stranded fragments of the same chain, separated by a helical fragment ...
Zok Tomasz +5 more
doaj +2 more sources
On the Coloring of Pseudoknots [PDF]
Journal of Knot Theory and Its Ramifications, 2013 Pseudodiagrams are diagrams of knots where some information about which strand goes over/under at certain crossings may be missing. Pseudoknots are equivalence classes of pseudodiagrams, with equivalence defined by a class of Reidemeister-type moves.
Henrich, Allison, Jablan, Slavik
core +2 more sources
Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot [PDF]
Proceedings of the National Academy of Sciences of the United States of America, 2017 The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability and dynamics.
Ansari, Anjum +7 more
core +5 more sources
Grow and Graft a Better CUDA pknotsRG for RNA Pseudoknot Free Energy Calculation [PDF]
Nucleic Acids Research, 2015 Most ab initio pseudoknot predicting methods provide very few folding scenarios for a given RNA sequence and have low sensitivities. RNA researchers, in many cases, would rather sacrifice the specificity for a much higher sensitivity for pseudoknot detection.
W. Langdon, M. Harman
semanticscholar +3 more sources
Insights into factorless translational initiation by the tRNA-like pseudoknot domain of a viral IRES. [PDF]
PLoS ONE, 2012 The intergenic region internal ribosome entry site (IGR IRES) of the Dicistroviridae family adopts an overlapping triple pseudoknot structure to directly recruit the 80S ribosome in the absence of initiation factors.
Hilda H T Au, Eric Jan
doaj +3 more sources