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

TitleDirect-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction.
Publication TypeJournal Article
Year of Publication2015
AuthorsDe Leonardis, E, Lutz, B, Ratz, S, Cocco, S, Monasson, R, Schug, A, Weigt, M
JournalNucleic Acids Res
Volume43
Issue21
Start Page10444
Pagination10444-10455
Date Published2015 Sep 29
ISSN1362-4962
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 modeling tools, systematically improved tertiary structure predictions can be obtained, as compared to using secondary structure information alone.

DOI10.1093/nar/gkv932
Alternate JournalNucleic Acids Res.
PubMed ID26420827