RNAiFold2T: Constraint Programming design of thermo-IRES switches
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Peter Clote | Juan Antonio García-Martín | Iván Dotú | Javier Fernandez-Chamorro | Gloria Lozano | Jorge Ramajo | Encarnacion Martinez-Salas | P. Clote | Iván Dotú | J. A. García-Martín | E. Martínez-Salas | Gloria Lozano | Javier Fernandez-Chamorro | Jorge Ramajo | Javier Fernández-Chamorro
[1] David H. Mathews,et al. RNAstructure: software for RNA secondary structure prediction and analysis , 2010, BMC Bioinformatics.
[2] E. Martínez-Salas,et al. Gemin5 promotes IRES interaction and translation control through its C-terminal region , 2012, Nucleic acids research.
[3] F. Narberhaus,et al. Bacterial RNA thermometers: molecular zippers and switches , 2012, Nature Reviews Microbiology.
[4] M. Macias,et al. Identification of novel non-canonical RNA-binding sites in Gemin5 involved in internal initiation of translation , 2014, Nucleic acids research.
[5] D. Mathews,et al. Accurate SHAPE-directed RNA structure determination , 2009, Proceedings of the National Academy of Sciences.
[6] H. Schwalbe,et al. Translation on demand by a simple RNA-based thermosensor , 2010, Nucleic acids research.
[7] Peter Clote,et al. Rnaifold: a Constraint Programming Algorithm for RNA inverse Folding and molecular Design , 2013, J. Bioinform. Comput. Biol..
[8] Markus Wieland,et al. RNA quadruplex-based modulation of gene expression. , 2007, Chemistry & biology.
[9] Jotun Hein,et al. Frnakenstein: multiple target inverse RNA folding , 2012, BMC Bioinformatics.
[10] E. Martínez-Salas,et al. Magnesium‐dependent folding of a picornavirus IRES element modulates RNA conformation and eIF4G interaction , 2014, The FEBS journal.
[11] N. Kotov,et al. Thermometer design at the nanoscale , 2007 .
[12] Kevin P. Murphy,et al. Efficient parameter estimation for RNA secondary structure prediction , 2007, ISMB/ECCB.
[13] Torsten Waldminghaus,et al. Genome-wide bioinformatic prediction and experimental evaluation of potential RNA thermometers , 2007, Molecular Genetics and Genomics.
[14] I. Rouzina,et al. Heat capacity effects on the melting of DNA. 1. General aspects. , 1999, Biophysical journal.
[15] E. Martínez-Salas,et al. Structural insights into viral IRES-dependent translation mechanisms. , 2015, Current opinion in virology.
[16] P. Stadler,et al. Design of Multi-Stable RNA Molecules , 2000 .
[17] Peter Clote,et al. Using RNA inverse folding to identify IRES-like structural subdomains , 2013, RNA biology.
[18] M. Inouye,et al. Escherichia coli CspA-family RNA chaperones are transcription antiterminators. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[19] Emma Kreuger,et al. Temperature-controlled Structural Alterations of an RNA Thermometer* , 2003, Journal of Biological Chemistry.
[20] P. Stadler,et al. Design of multistable RNA molecules. , 2001, RNA.
[21] Harald Schwalbe,et al. Modulation of the stability of the Salmonella fourU-type RNA thermometer , 2011, Nucleic acids research.
[22] Peter Clote,et al. RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules , 2015, Nucleic Acids Res..
[23] Eduardo Eyras,et al. Structural basis for the biological relevance of the invariant apical stem in IRES-mediated translation , 2011, Nucleic acids research.
[24] Tae Seok Moon,et al. De novo design of heat-repressible RNA thermosensors in E. coli , 2015, Nucleic acids research.
[25] Torsten Waldminghaus,et al. FourU: a novel type of RNA thermometer in Salmonella , 2007, Molecular microbiology.
[26] Peter Clote,et al. Complete RNA inverse folding: computational design of functional hammerhead ribozymes , 2014, Nucleic acids research.
[27] H. Hennecke,et al. A mRNA-based thermosensor controls expression of rhizobial heat shock genes. , 2001, Nucleic acids research.
[28] Robert M. Dirks,et al. Paradigms for computational nucleic acid design. , 2004, Nucleic acids research.
[29] J. McCaskill. The equilibrium partition function and base pair binding probabilities for RNA secondary structure , 1990, Biopolymers.
[30] P. Schuster,et al. Generic properties of combinatory maps: neutral networks of RNA secondary structures. , 1997, Bulletin of mathematical biology.
[31] Niles A. Pierce,et al. Nucleic acid sequence design via efficient ensemble defect optimization , 2011, J. Comput. Chem..
[32] Dmitrij Frishman,et al. RNAtips: analysis of temperature-induced changes of RNA secondary structure , 2013, Nucleic Acids Res..
[33] Robert D. Finn,et al. Rfam 12.0: updates to the RNA families database , 2014, Nucleic Acids Res..
[34] David H. Mathews,et al. NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure , 2009, Nucleic Acids Res..
[35] Michael Zuker,et al. Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..
[36] E. Pedroso,et al. Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation , 2015, RNA biology.
[37] F. Narberhaus,et al. Thermozymes: Synthetic RNA thermometers based on ribozyme activity. , 2013, RNA biology.
[38] Torsten Waldminghaus,et al. Generation of synthetic RNA-based thermosensors , 2008, Biological chemistry.
[39] Peter F. Stadler,et al. ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.
[40] G. Balogh,et al. Synechocystis HSP17 is an amphitropic protein that stabilizes heat-stressed membranes and binds denatured proteins for subsequent chaperone-mediated refolding , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[41] Juliane Neupert,et al. Design of simple synthetic RNA thermometers for temperature-controlled gene expression in Escherichia coli , 2008, Nucleic acids research.
[42] Peter Clote,et al. Integrating Chemical Footprinting Data into RNA Secondary Structure Prediction , 2012, PloS one.
[43] S. Altuvia,et al. Alternative mRNA structures of the cIII gene of bacteriophage lambda determine the rate of its translation initiation. , 1989, Journal of molecular biology.
[44] P. Cossart,et al. An RNA Thermosensor Controls Expression of Virulence Genes in Listeria monocytogenes , 2002, Cell.
[45] E. Beck,et al. Functional analysis of the internal translation initiation site of foot-and-mouth disease virus , 1990, Journal of virology.
[46] M. Waterman. Secondary Structure of Single-Stranded Nucleic Acidst , 1978 .
[47] P. Stadler,et al. De novo design of a synthetic riboswitch that regulates transcription termination , 2012, Nucleic acids research.
[48] Atsushi Ogawa,et al. Rational design of artificial riboswitches based on ligand-dependent modulation of internal ribosome entry in wheat germ extract and their applications as label-free biosensors. , 2011, RNA.
[49] Alexander Churkin,et al. RNAthermsw: Direct Temperature Simulations for Predicting the Location of RNA Thermometers , 2014, PloS one.