Results 1 to 10 of about 14,400 (274)

Pseudoknots in a Homopolymer [PDF]

Phys. Rev. E 70, 011802 (2004), 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. Although the total number of pseudoknots is extensive at all temperatures, we find that the number of ...
Kabakcioglu, A., Stella, A. L.
arxiv   +9 more sources

The Theory of Pseudoknots [PDF]

Journal of Knot Theory and Its Ramifications, June 2013, Vol. 22, No. 7, 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 point.
Henrich, Allison, Hoberg, Rebecca, Jablan, Slavik, Johnson, Lee, Minten, Elizabeth, Radovic, Ljiljana   +5 more
arxiv   +7 more sources

On the Coloring of Pseudoknots [PDF]

arXiv, 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. In this paper, we introduce two natural extensions of classical knot colorability to this broader class
Henrich, Allison, Jablan, Slavik
arxiv   +6 more sources

Prediction of RNA pseudoknots by Monte Carlo simulations [PDF]

arXiv, 2004
In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the non-planar topologies of RNA structures and propose a classification of RNA pseudoknots according to the minimal ...
Orland, H., Vernizzi, G., Zee, A.
arxiv   +6 more sources

Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations [PDF]

Proceedings of the National Academy of Sciences USA 100 (2003) 15310-15315, 2003
Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA folding simulations, which follow the stochastic closing and opening of individual RNA helices.
A. Xayaphoummine, Evers, F. Thalmann, Ferr  -D'Amar  , Giedroc, Gultyaev, H. Isambert, Higgs, Lehnert, Mathews, McCaskill, Mironov, Pan, Pleij, Rivas, Russell, Sclavi, Shirts, T. Bucher, Tinoco, Treiber, Zarrinkar, Zuker   +22 more
arxiv   +5 more sources

Improved RNA pseudoknots prediction and classification using a new topological invariant [PDF]

Phys. Rev. E 94, 042410 (2016), 2016
We propose a new topological characterization of RNA secondary structures with pseudoknots based on two topological invariants. Starting from the classic arc-representation of RNA secondary structures, we consider a model that couples both I) the topological genus of the graph and II) the number of crossing arcs of the corresponding primitive graph. We
Orland, Henri, Vernizzi, Graziano, Zee, A.   +2 more
arxiv   +5 more sources

TT2NE: A novel algorithm to predict RNA secondary structures with pseudoknots [PDF]

arXiv, 2010
We present TT2NE, a new algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. TT2NE guarantees to find the minimum free energy structure irrespectively of pseudoknot topology. This unique proficiency is obtained at the expense of the maximum length
Bailor, Bellaousov, Bon, Dam, Dirks, Doshi, Elliot, Friedman, Henri Orland, Kuo, Lyngso, Mathews, McCaskill, Metzler, Michaël Bon, Nussinov, Orland, Pillsbury, Reeder, Ren, Rivas, Rivas, Ruan, Shen, t'Hooft, Tinoco, Vernizzi, Zhao, Zuker, Zuker   +29 more
arxiv   +7 more sources

RNA denaturation: excluded volume, pseudoknots and transition scenarios [PDF]

Phys. Rev Lett. 91, 198102 (2003), 2003
A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous transition. Otherwise a smooth crossover occurs from the swollen linear polymer behavior to highly ramified, almost ...
A. L. Stella, B. Li, C. Vanderzande, E. Orlandini, E. Rivas, I. L. Hofacker, M. Baiesi, M. Zuker, M. C. Tesi, P.-G. de Gennes, R. Bundschuh, S. B. Smith, V. Privman   +12 more
arxiv   +4 more sources

The internal initiation of translation in bovine viral diarrhea virus RNA depends on the presence of an RNA pseudoknot upstream of the initiation codon [PDF]

Virology Journal, 2007
Background Bovine viral diarrhea virus (BVDV) is the prototype representative of the pestivirus genus in the Flaviviridae family. It has been shown that the initiation of translation of BVDV RNA occurs by an internal ribosome entry mechanism mediated by ...
Moes Lorin, Wirth Manfred
doaj   +2 more sources

Predicting RNA Secondary Structures with Arbitrary Pseudoknots by Maximizing the Number of Stacking Pairs [PDF]

arXiv, 2001
The paper investigates the computational problem of predicting RNA secondary structures. The general belief is that allowing pseudoknots makes the problem hard. Existing polynomial-time algorithms are heuristic algorithms with no performance guarantee and can only handle limited types of pseudoknots.
Samuel Ieong, Ming‐Yang Kao, Tak‐Wah Lam, Wing‐Kin Sung, Siu‐Ming Yiu   +4 more
arxiv   +3 more sources