Literature DB >> 15904268

Enumeration of RNA structures by matrix models.

Graziano Vernizzi1, Henri Orland, A Zee.   

Abstract

We enumerate the number of RNA contact structures according to their genus, i.e., the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for the simple case of an RNA molecule with an infinitely flexible backbone, in which any arbitrary pair of bases is allowed. We analyze the distribution of the genus of pseudoknots as a function of the total number of nucleotides along the phosphate-sugar backbone.

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Year:  2005        PMID: 15904268     DOI: 10.1103/PhysRevLett.94.168103

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  11 in total

1.  On the page number of RNA secondary structures with pseudoknots.

Authors:  Peter Clote; Stefan Dobrev; Ivan Dotu; Evangelos Kranakis; Danny Krizanc; Jorge Urrutia
Journal:  J Math Biol       Date:  2011-12-10       Impact factor: 2.259

2.  Structural and thermodynamic properties of a linearly perturbed matrix model for RNA folding.

Authors:  I Garg; N Deo
Journal:  Eur Phys J E Soft Matter       Date:  2010-11-18       Impact factor: 1.890

3.  Counting RNA pseudoknotted structures.

Authors:  Cédric Saule; Mireille Régnier; Jean-Marc Steyaert; Alain Denise
Journal:  J Comput Biol       Date:  2011-05-06       Impact factor: 1.479

4.  The block spectrum of RNA pseudoknot structures.

Authors:  Thomas J X Li; Christie S Burris; Christian M Reidys
Journal:  J Math Biol       Date:  2019-06-06       Impact factor: 2.259

5.  Statistics of topological RNA structures.

Authors:  Thomas J X Li; Christian M Reidys
Journal:  J Math Biol       Date:  2016-11-16       Impact factor: 2.259

6.  Combinatorics of locally optimal RNA secondary structures.

Authors:  Eric Fusy; Peter Clote
Journal:  J Math Biol       Date:  2012-12-22       Impact factor: 2.259

7.  Topological classification and enumeration of RNA structures by genus.

Authors:  J E Andersen; R C Penner; C M Reidys; M S Waterman
Journal:  J Math Biol       Date:  2012-10-02       Impact factor: 2.259

8.  Shapes of interacting RNA complexes.

Authors:  Benjamin M M Fu; Christian M Reidys
Journal:  J Comput Biol       Date:  2014-07-30       Impact factor: 1.479

9.  Genus for biomolecules.

Authors:  Paweł Rubach; Sebastian Zajac; Borys Jastrzebski; Joanna I Sulkowska; Piotr Sułkowski
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

10.  TT2NE: a novel algorithm to predict RNA secondary structures with pseudoknots.

Authors:  Michaël Bon; Henri Orland
Journal:  Nucleic Acids Res       Date:  2011-05-18       Impact factor: 16.971

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