Results 11 to 20 of about 14,795 (267)
Pseudoknots in a Homopolymer [PDF]
Physical Review E, 2003 After a discussion of the definition and number of pseudoknots, we reconsider the self-attracting homopolymer paying particular attention to the scaling of the number of pseudoknots at different temperature regimes in two and three dimensions.
Kabakcioglu, A., Stella, A. L.
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Inverse folding of RNA pseudoknot structures [PDF]
Algorithms for Molecular Biology, 2010 Background RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and G-U-base pairings (secondary structure) and additional cross-serial base pairs.
Li Linda YM +2 more
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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
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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
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An efficient simulated annealing algorithm for the RNA secondary structure prediction with Pseudoknots [PDF]
BMC Genomics, 2019 Background RNA pseudoknot structures play an important role in biological processes. However, existing RNA secondary structure prediction algorithms cannot predict the pseudoknot structure efficiently.
Zhang Kai +4 more
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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
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Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension [PDF]
Journal of Molecular Biology, 2016 Because of the potential link between -1 programmed ribosomal frameshifting and response of a pseudoknot (PK) RNA to force, a number of single molecule pulling experiments have been performed on PKs to decipher the mechanism of programmed ribosomal ...
Denesyuk, Natalia A. +2 more
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A steepest descent calculation of RNA pseudoknots [PDF]
Physical Review E, 2002 We enumerate possible topologies of pseudoknots in single-stranded RNA molecules. We use a steepest-descent approximation in the large N matrix field theory, and a Feynman diagram formalism to describe the resulting pseudoknot ...
A. Zee +3 more
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jViz.RNA 4.0-Visualizing pseudoknots and RNA editing employing compressed tree graphs.
PLoS ONE, 2019 Previously, we have introduced an improved version of jViz.RNA which enabled faster and more stable RNA visualization by employing compressed tree graphs.
Boris Shabash, Kay C Wiese
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Possible involvement of three-stemmed pseudoknots in regulating translational initiation in human mRNAs. [PDF]
PLoS ONERNA pseudoknots play a crucial role in various cellular functions. Established pseudoknots show significant variation in both size and structural complexity. Specifically, three-stemmed pseudoknots are characterized by an additional stem-loop embedded in
Xiaolan Huang, Zhihua Du
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