Literature DB >> 17548241

RNA structure: bioinformatic analysis.

Fabrice Jossinet1, Thomas E Ludwig, Eric Westhof.   

Abstract

The range of functions ascribed to RNA molecules has grown considerably during recent years. Consequently, the analysis and comparison of RNA sequences have become recurrent tasks in molecular biology. Because the biological function of an RNA is expressed more by its folded architecture than by its sequence, original computational tools adapted to the multifaceted RNA functions have to be developed. Such tools, recently published, enable a user to solve classical problems related to RNA research: constructing 'structural' multiple alignments, inferring complete structures and structural motifs from RNA alignments, or searching structural homology in genomic databases.

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Year:  2007        PMID: 17548241     DOI: 10.1016/j.mib.2007.05.010

Source DB:  PubMed          Journal:  Curr Opin Microbiol        ISSN: 1369-5274            Impact factor:   7.934


  18 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.  Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy.

Authors:  Nathan J Baird; Steven J Ludtke; Htet Khant; Wah Chiu; Tao Pan; Tobin R Sosnick
Journal:  J Am Chem Soc       Date:  2010-11-01       Impact factor: 15.419

3.  From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal.

Authors:  Sandra Smit; Kristian Rother; Jaap Heringa; Rob Knight
Journal:  RNA       Date:  2008-01-29       Impact factor: 4.942

4.  Predicting structures and stabilities for H-type pseudoknots with interhelix loops.

Authors:  Song Cao; Shi-Jie Chen
Journal:  RNA       Date:  2009-02-23       Impact factor: 4.942

5.  RNA nanotechnology for computer design and in vivo computation.

Authors:  Meikang Qiu; Emil Khisamutdinov; Zhengyi Zhao; Cheryl Pan; Jeong-Woo Choi; Neocles B Leontis; Peixuan Guo
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2013-09-02       Impact factor: 4.226

6.  In silico 'fishing' using known small regulatory RNA (sRNA) candidates as the decoy from Escherichia coli, Salmonella typhi and Salmonella typhimurium manifested 14 novel sRNA candidates in the orthologous region of Proteus mirabilis.

Authors:  Selvaraju KishanRaj; Samuggam Sumitha; Balakrishnan Siventhiran; Othayakumar Thiviyaa; Kathiresan V Sathasivam; Rathinam Xavier; Thean-Hock Tang; Marimuthu Citartan; Suresh V Chinni
Journal:  Mol Biol Rep       Date:  2018-10-03       Impact factor: 2.316

7.  The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex.

Authors:  Xiang-Jun Lu; Wilma K Olson; Harmen J Bussemaker
Journal:  Nucleic Acids Res       Date:  2010-03-11       Impact factor: 16.971

8.  Dual-channel single-molecule fluorescence resonance energy transfer to establish distance parameters for RNA nanoparticles.

Authors:  Dan Shu; Hui Zhang; Roman Petrenko; Jarek Meller; Peixuan Guo
Journal:  ACS Nano       Date:  2010-10-18       Impact factor: 15.881

9.  Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'.

Authors:  Michelle M Meyer; Tyler D Ames; Daniel P Smith; Zasha Weinberg; Michael S Schwalbach; Stephen J Giovannoni; Ronald R Breaker
Journal:  BMC Genomics       Date:  2009-06-16       Impact factor: 3.969

10.  Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis.

Authors:  Roberto T Arrial; Roberto C Togawa; Marcelo de M Brigido
Journal:  BMC Bioinformatics       Date:  2009-08-04       Impact factor: 3.169

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