Literature DB >> 15529172

How do RNA folding algorithms work?

Sean R Eddy1.   

Abstract

Programs such as MFOLD and ViennaRNA are widely used to predict RNA secondary structures. How do these algorithms work? Why can't they predict RNA pseudoknots? How accurate are they, and will they get better?

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Year:  2004        PMID： 15529172     DOI： 10.1038/nbt1104-1457

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


  41 in total

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2.  Heuristic RNA pseudoknot prediction including intramolecular kissing hairpins.

Authors:  Jana Sperschneider; Amitava Datta; Michael J Wise
Journal:  RNA       Date:  2010-11-22       Impact factor: 4.942

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4.  Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions.

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Review 5.  Advances in RNA structure prediction from sequence: new tools for generating hypotheses about viral RNA structure-function relationships.

Authors:  Susan J Schroeder
Journal:  J Virol       Date:  2009-04-15       Impact factor: 5.103

6.  Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms.

Authors:  Feng Ding; Shantanu Sharma; Poornima Chalasani; Vadim V Demidov; Natalia E Broude; Nikolay V Dokholyan
Journal:  RNA       Date:  2008-05-02       Impact factor: 4.942

7.  RNA secondary structure prediction.

Authors:  David H Mathews; Douglas H Turner; Michael Zuker
Journal:  Curr Protoc Nucleic Acid Chem       Date:  2007-03

8.  RNA secondary structure analysis using RNAstructure.

Authors:  David H Mathews
Journal:  Curr Protoc Bioinformatics       Date:  2006-03

9.  Lack of secondary structure characterizes the 5' ends of mammalian mitochondrial mRNAs.

Authors:  Christie N Jones; Kevin A Wilkinson; Kimberly T Hung; Kevin M Weeks; Linda L Spremulli
Journal:  RNA       Date:  2008-03-26       Impact factor: 4.942

10.  Structural characterization of the internal transcribed spacer 2 (ITS2) of the ribosomal DNA (rDNA) cluster in Calyptratae (Diptera: Schizophora) and its implications for molecular phylogenetic analyses.

Authors:  M A T Marinho; A M L Azeredo-Espin; N I T Zanchin
Journal:  J Mol Evol       Date:  2013-02-19       Impact factor: 2.395
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