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 modeling tools, systematically improved terti

SUBMITTER: De Leonardis E 

PROVIDER: S-EPMC4666395 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature