Literature DB >> 1710343

A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison.

M Zuker1, J A Jaeger, D H Turner.   

Abstract

This article describes the latest version of an RNA folding algorithm that predicts both optimal and suboptimal solutions based on free energy minimization. A number of RNA's with known structures deduced from comparative sequence analysis are folded to test program performance. The group of solutions obtained for each molecule is analysed to determine how many of the known helixes occur in the optimal solution and in the best suboptimal solution. In most cases, a structure about 80% correct is found with a free energy within 2% of the predicted lowest free energy structure.

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Year:  1991        PMID： 1710343      PMCID： PMC328190          DOI： 10.1093/nar/19.10.2707

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  32 in total

1.  Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns.

Authors:  F Michel; A D Ellington; S Couture; J W Szostak
Journal:  Nature       Date:  1990-10-11       Impact factor: 49.962

2.  Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops".

Authors:  C R Woese; S Winker; R R Gutell
Journal:  Proc Natl Acad Sci U S A       Date:  1990-11       Impact factor: 11.205

3.  Effects of GA mismatches on the structure and thermodynamics of RNA internal loops.

Authors:  J SantaLucia; R Kierzek; D H Turner
Journal:  Biochemistry       Date:  1990-09-18       Impact factor: 3.162

4.  Polymer-supported RNA synthesis and its application to test the nearest-neighbor model for duplex stability.

Authors:  R Kierzek; M H Caruthers; C E Longfellow; D Swinton; D H Turner; S M Freier
Journal:  Biochemistry       Date:  1986-12-02       Impact factor: 3.162

5.  Long-range intron-exon and intron-intron pairings involved in self-splicing of class II catalytic introns.

Authors:  F Michel; A Jacquier
Journal:  Cold Spring Harb Symp Quant Biol       Date:  1987

6.  A dynamic programming algorithm for finding alternative RNA secondary structures.

Authors:  A L Williams; I Tinoco
Journal:  Nucleic Acids Res       Date:  1986-01-10       Impact factor: 16.971

7.  Structural conservation among three homologous introns of bacteriophage T4 and the group I introns of eukaryotes.

Authors:  D A Shub; J M Gott; M Q Xu; B F Lang; F Michel; J Tomaschewski; J Pedersen-Lane; M Belfort
Journal:  Proc Natl Acad Sci U S A       Date:  1988-02       Impact factor: 11.205

8.  Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro.

Authors:  J R Sampson; O C Uhlenbeck
Journal:  Proc Natl Acad Sci U S A       Date:  1988-02       Impact factor: 11.205

9.  Structure of yeast phenylalanine tRNA at 3 A resolution.

Authors:  J D Robertus; J E Ladner; J T Finch; D Rhodes; R S Brown; B F Clark; A Klug
Journal:  Nature       Date:  1974-08-16       Impact factor: 49.962

10.  Higher order structure of chloroplastic 5S ribosomal RNA from spinach.

Authors:  P Romby; E Westhof; R Toukifimpa; R Mache; J P Ebel; C Ehresmann; B Ehresmann
Journal:  Biochemistry       Date:  1988-06-28       Impact factor: 3.162
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  62 in total

1.  Identifying ribozyme-accessible sites using NUH triplet-targeting gapmers.

Authors:  A A Mir; T J Lockett; P Hendry
Journal:  Nucleic Acids Res       Date:  2001-05-01       Impact factor: 16.971

2.  Analysis of elements involved in pseudoknot-dependent expression and regulation of the repA gene of an IncL/M plasmid.

Authors:  V Athanasopoulos; J Praszkier; A J Pittard
Journal:  J Bacteriol       Date:  1999-03       Impact factor: 3.490

3.  Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble.

Authors:  Emily Rogers; Christine E Heitsch
Journal:  Nucleic Acids Res       Date:  2014-11-11       Impact factor: 16.971

4.  External-loop free energy affects dye-labeled terminators premature terminations in DNA cycle-sequencing reactions.

Authors:  Long Wen
Journal:  Mol Biotechnol       Date:  2002-11       Impact factor: 2.695

5.  Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops.

Authors:  V P Antao; I Tinoco
Journal:  Nucleic Acids Res       Date:  1992-02-25       Impact factor: 16.971

6.  The human immunodeficiency virus type 1 packaging signal and major splice donor region have a conserved stable secondary structure.

Authors:  G P Harrison; A M Lever
Journal:  J Virol       Date:  1992-07       Impact factor: 5.103

7.  Predicted secondary structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): impact on sequence alignment and phylogeny estimation.

Authors:  Joseph J Gillespie; Matthew J Yoder; Robert A Wharton
Journal:  J Mol Evol       Date:  2005-07-14       Impact factor: 2.395

8.  Specific requirements for elements of the 5' and 3' terminal regions in flavivirus RNA synthesis and viral replication.

Authors:  Li Yu; Masako Nomaguchi; R Padmanabhan; Lewis Markoff
Journal:  Virology       Date:  2008-01-29       Impact factor: 3.616

9.  Large deviations for random trees and the branching of RNA secondary structures.

Authors:  Yuri Bakhtin; Christine E Heitsch
Journal:  Bull Math Biol       Date:  2008-12-13       Impact factor: 1.758

10.  The effects of hairpin loops on ligand-DNA interactions.

Authors:  Binh Nguyen; W David Wilson
Journal:  J Phys Chem B       Date:  2009-10-29       Impact factor: 2.991
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