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Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction

Abstract : Despite the biological importance of non-coding RNA, their structural characterization remains challenging. Making use of the rapidly growing sequence databases, we analyze nucleotide coevolution across homologous sequences via Direct-Coupling Analysis to detect nucleotide-nucleotide contacts. For a representative set of riboswitches, we show that the results of Direct-Coupling Analysis in combination with a generalized Nussinov algorithm systematically improve the results of RNA secondary structure prediction beyond traditional covariance approaches based on mutual information. Even more importantly, we show that the results of Direct-Coupling Analysis are enriched in tertiary structure contacts. By integrating these predictions into molecular model-ing tools, systematically improved tertiary structure predictions can be obtained, as compared to using secondary structure information alone.
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Eleonora De leonardis, Benjamin Lutz, Sebastian Ratz, Simona Cocco, Rémi Monasson, et al.. Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction. Nucleic Acids Research, Oxford University Press, 2015, 43 (21), pp.10444-10455. ⟨10.1093/nar/gkv932⟩. ⟨hal-01271548⟩

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