Literature DB >> 19369331

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

Susan J Schroeder1.   

Abstract

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Year:  2009        PMID： 19369331      PMCID： PMC2698544          DOI： 10.1128/JVI.00251-09

Source DB:  PubMed          Journal:  J Virol        ISSN： 0022-538X            Impact factor:   5.103


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  108 in total

1.  Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops.

Authors:  David H Mathews; Douglas H Turner
Journal:  Biochemistry       Date:  2002-01-22       Impact factor: 3.162

2.  Dynalign: an algorithm for finding the secondary structure common to two RNA sequences.

Authors:  David H Mathews; Douglas H Turner
Journal:  J Mol Biol       Date:  2002-03-22       Impact factor: 5.469

3.  RnaViz 2: an improved representation of RNA secondary structure.

Authors:  Peter De Rijk; Jan Wuyts; Rupert De Wachter
Journal:  Bioinformatics       Date:  2003-01-22       Impact factor: 6.937

4.  Rfam: an RNA family database.

Authors:  Sam Griffiths-Jones; Alex Bateman; Mhairi Marshall; Ajay Khanna; Sean R Eddy
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

5.  The role of site accessibility in microRNA target recognition.

Authors:  Michael Kertesz; Nicola Iovino; Ulrich Unnerstall; Ulrike Gaul; Eran Segal
Journal:  Nat Genet       Date:  2007-09-23       Impact factor: 38.330

6.  Effect of target secondary structure on RNAi efficiency.

Authors:  Yu Shao; Chi Yu Chan; Anil Maliyekkel; Charles E Lawrence; Igor B Roninson; Ye Ding
Journal:  RNA       Date:  2007-08-07       Impact factor: 4.942

7.  Automated de novo prediction of native-like RNA tertiary structures.

Authors:  Rhiju Das; David Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2007-08-28       Impact factor: 11.205

8.  Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution.

Authors:  Martin Egli; George Minasov; Li Su; Alexander Rich
Journal:  Proc Natl Acad Sci U S A       Date:  2002-03-19       Impact factor: 11.205

9.  The 5' and 3' extremities of the satellite tobacco necrosis virus translational enhancer domain contribute differentially to stimulation of translation.

Authors:  Rosalinde van Lipzig; Alexander P Gultyaev; Cornelis W A Pleij; Marc van Montagu; Marc Cornelissen; Frank Meulewaeter
Journal:  RNA       Date:  2002-02       Impact factor: 4.942

10.  Encapsidation of nanoparticles by red clover necrotic mosaic virus.

Authors:  LiNa Loo; Richard H Guenther; Steven A Lommel; Stefan Franzen
Journal:  J Am Chem Soc       Date:  2007-08-18       Impact factor: 15.419
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  28 in total

1.  Site-specific platinum(II) cross-linking in a ribozyme active site.

Authors:  Erich G Chapman; Victoria J DeRose
Journal:  J Am Chem Soc       Date:  2011-12-14       Impact factor: 15.419

2.  Key genomic changes necessary for an in vivo lethal mouse marburgvirus variant selection process.

Authors:  Loreen L Lofts; Jay B Wells; Sina Bavari; Kelly L Warfield
Journal:  J Virol       Date:  2011-02-02       Impact factor: 5.103

3.  StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo.

Authors:  Yin Tang; Emil Bouvier; Chun Kit Kwok; Yiliang Ding; Anton Nekrutenko; Philip C Bevilacqua; Sarah M Assmann
Journal:  Bioinformatics       Date:  2015-04-16       Impact factor: 6.937

4.  Ensemble of secondary structures for encapsidated satellite tobacco mosaic virus RNA consistent with chemical probing and crystallography constraints.

Authors:  Susan J Schroeder; Jonathan W Stone; Samuel Bleckley; Theodore Gibbons; Deborah M Mathews
Journal:  Biophys J       Date:  2011-07-06       Impact factor: 4.033

5.  Identification of potential conserved RNA secondary structure throughout influenza A coding regions.

Authors:  Walter N Moss; Salvatore F Priore; Douglas H Turner
Journal:  RNA       Date:  2011-05-02       Impact factor: 4.942

Review 6.  SHAPE-directed RNA secondary structure prediction.

Authors:  Justin T Low; Kevin M Weeks
Journal:  Methods       Date:  2010-06-08       Impact factor: 3.608

Review 7.  Computational approaches to 3D modeling of RNA.

Authors:  Christian Laing; Tamar Schlick
Journal:  J Phys Condens Matter       Date:  2010-06-15       Impact factor: 2.333

8.  Dengue virus markers of virulence and pathogenicity.

Authors:  Rebeca Rico-Hesse
Journal:  Future Virol       Date:  2009-11-01       Impact factor: 1.831

9.  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

10.  Natural insertions within the N-terminal region of the coat protein of Maize dwarf mosaic potyvirus (MDMV) have an effect on the RNA stability.

Authors:  Kathrin Petrik; Endre Sebestyén; Gyöngyvér Gell; Ervin Balázs
Journal:  Virus Genes       Date:  2009-11-24       Impact factor: 2.332
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