Literature DB >> 10334330

An approximation of loop free energy values of RNA H-pseudoknots.

A P Gultyaev, F H van Batenburg, C W Pleij.   

Abstract

A set of free energy values is suggested for RNA H-pseudoknot loops. The parameters are adjusted to be consistent with the theory of polymer thermodynamics and known data on pseudoknots. The values can be used for estimates of pseudoknot stabilities and computer predictions of RNA structures.

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Year:  1999        PMID： 10334330      PMCID： PMC1369787          DOI： 10.1017/s135583829998189x

Source DB:  PubMed          Journal:  RNA        ISSN： 1355-8382            Impact factor:   4.942


  34 in total

1.  Programmed ribosomal frameshifting: much ado about knotting!

Authors:  S L Alam; J F Atkins; R F Gesteland
Journal:  Proc Natl Acad Sci U S A       Date:  1999-12-07       Impact factor: 11.205

2.  PseudoBase: a database with RNA pseudoknots.

Authors:  F H van Batenburg; A P Gultyaev; C W Pleij; J Ng; J Oliehoek
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

3.  Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme.

Authors:  H Isambert; E D Siggia
Journal:  Proc Natl Acad Sci U S A       Date:  2000-06-06       Impact factor: 11.205

4.  Sequence comparison and secondary structure analysis of the 3' noncoding region of flavivirus genomes reveals multiple pseudoknots.

Authors:  R C Olsthoorn; J F Bol
Journal:  RNA       Date:  2001-10       Impact factor: 4.942

5.  Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations.

Authors:  A Xayaphoummine; T Bucher; F Thalmann; H Isambert
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-15       Impact factor: 11.205

6.  A domain-based model for predicting large and complex pseudoknotted structures.

Authors:  Song Cao; Shi-Jie Chen
Journal:  RNA Biol       Date:  2012-02-01       Impact factor: 4.652

7.  ProbKnot: fast prediction of RNA secondary structure including pseudoknots.

Authors:  Stanislav Bellaousov; David H Mathews
Journal:  RNA       Date:  2010-08-10       Impact factor: 4.942

8.  Computing the conformational entropy for RNA folds.

Authors:  Liang Liu; Shi-Jie Chen
Journal:  J Chem Phys       Date:  2010-06-21       Impact factor: 3.488

9.  Statistical thermodynamics for chain molecules with simple RNA tertiary contacts.

Authors:  Zoia Kopeikin; Shi-Jie Chen
Journal:  J Chem Phys       Date:  2005-03-01       Impact factor: 3.488

10.  Folding thermodynamics of pseudoknotted chain conformations.

Authors:  Zoia Kopeikin; Shi-Jie Chen
Journal:  J Chem Phys       Date:  2006-04-21       Impact factor: 3.488
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