Journal
NUCLEIC ACIDS RESEARCH
Volume 43, Issue 21, Pages 10444-10455Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkv932
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Funding
- Agence Nationale de la Recherche project COEVSTAT [ANR-13-BS04-0012-01]
- Impuls- and Vernetzungsfond of the Helmholtz Association
- Deutsche Forschungsgemeinschaft
- Karlsruher Institut fur Technologie
- Agence Nationale de la Recherche (ANR) [ANR-13-BS04-0012] Funding Source: Agence Nationale de la Recherche (ANR)
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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.
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