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RNA Biology Volume 10, 2013 - Issue 12
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Research Paper

Using RNA inverse folding to identify IRES-like structural subdomains

Ivan Dotu Biology Department; Boston College; Chestnut Hill, MA USA
,
Gloria Lozano Centro de Biologia Molecular Severo Ochoa; Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid; Madrid, Spain
,
Peter Clote Biology Department; Boston College; Chestnut Hill, MA USA
&
Encarnacion Martinez-Salas Centro de Biologia Molecular Severo Ochoa; Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid; Madrid, SpainCorrespondence[email protected]
Pages 1842-1852 | Received 22 Aug 2013, Accepted 30 Oct 2013, Published online: 04 Nov 2013

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Rosario Francisco-Velilla, Azman Embarc-Buh, Sergio Rangel-Guerrero, Sudipto Basu, Sudip Kundu & Encarnacion Martinez-Salas. (2020) RNA-protein coevolution study of Gemin5 uncovers the role of the PXSS motif of RBS1 domain for RNA binding. RNA Biology 17:9, pages 1331-1341.
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Articles from other publishers (17)

Sumit Mukherjee, Matan Drory Retwitzer, Sara M Hubbell, Michelle M Meyer & Danny Barash. (2023) A computational approach for the identification of distant homologs of bacterial riboswitches based on inverse RNA folding. Briefings in Bioinformatics 24:3.
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Asmita Gupta & Manju Bansal. (2020) RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures. Briefings in Bioinformatics 21:4, pages 1151-1163.
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Matan Drory Retwitzer, Vladimir Reinharz, Alexander Churkin, Yann Ponty, Jérôme Waldispühl & Danny Barash. (2020) incaRNAfbinv 2.0 : a webserver and software with motif control for fragment-based design of RNAs . Bioinformatics 36:9, pages 2920-2922.
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Deepak Koirala, Yaming Shao, Yelena Koldobskaya, James R. Fuller, Andrew M. Watkins, Sandip A. Shelke, Evgeny V. Pilipenko, Rhiju Das, Phoebe A. Rice & Joseph A. Piccirilli. (2019) A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. Nature Communications 10:1.
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Gloria Lozano, Rosario Francisco-Velilla & Encarnacion Martinez-Salas. (2018) Deconstructing internal ribosome entry site elements: an update of structural motifs and functional divergences. Open Biology 8:11, pages 180155.
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Encarnacion Martinez-Salas, Rosario Francisco-Velilla, Javier Fernandez-Chamorro & Azman M. Embarek. (2018) Insights into Structural and Mechanistic Features of Viral IRES Elements. Frontiers in Microbiology 8.
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Alexander Churkin, Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl & Danny Barash. (2017) Design of RNAs: comparing programs for inverse RNA folding. Briefings in Bioinformatics, pages bbw120.
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Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl & Danny Barash. (2016) incaRNAfbinv : a web server for the fragment-based design of RNA sequences . Nucleic Acids Research 44:W1, pages W308-W314.
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Juan Antonio Garcia-Martin, Ivan Dotu, Javier Fernandez-Chamorro, Gloria Lozano, Jorge Ramajo, Encarnacion Martinez-Salas & Peter Clote. (2016) RNAiFold2T: Constraint Programming design of thermo-IRES switches. Bioinformatics 32:12, pages i360-i368.
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Javier Fernandez-Chamorro, Gloria Lozano, Juan Antonio Garcia-Martin, Jorge Ramajo, Ivan Dotu, Peter Clote & Encarnacion Martinez-Salas. (2016) Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements. Scientific Reports 6:1.
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Gloria Lozano, Noemi Fernandez & Encarnacion Martinez-Salas. (2016) Modeling Three-Dimensional Structural Motifs of Viral IRES. Journal of Molecular Biology 428:5, pages 767-776.
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Rosario Francisco-Velilla, Gloria Lozano, Rosa Diaz-Toledano, Javier Fernandez-Chamorro, Azman M. Embarek & Encarnacion Martinez-Salas. 2016. Evolution of the Protein Synthesis Machinery and Its Regulation. Evolution of the Protein Synthesis Machinery and Its Regulation 547 564 .
Encarnación Martínez-Salas, Rosario Francisco-Velilla, Javier Fernandez-Chamorro, Gloria Lozano & Rosa Diaz-Toledano. (2015) Picornavirus IRES elements: RNA structure and host protein interactions. Virus Research 206, pages 62-73.
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Juan Antonio Garcia-Martin, Ivan Dotu & Peter Clote. (2015) RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules. Nucleic Acids Research 43:W1, pages W513-W521.
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Gloria Lozano & Encarnación Martínez-Salas. (2015) Structural insights into viral IRES-dependent translation mechanisms. Current Opinion in Virology 12, pages 113-120.
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Augusto Samuel Jiménez-González, Noemí Fernández, Encarnación Martínez-Salas & Estela Sánchez de Jiménez. (2014) Functional and Structural Analysis of Maize Hsp101 IRES. PLoS ONE 9:9, pages e107459.
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Gloria Lozano, Noemi Fernandez & Encarnacion Martinez‐Salas. (2014) Magnesium‐dependent folding of a picornavirus IRES element modulates RNA conformation and eIF4G interaction . The FEBS Journal 281:16, pages 3685-3700.
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