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URN: urn:nbn:de:swb:90-514136

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

De Leonardis, Eleonora; Lutz, Benjamin; Ratz, Sebastian; Cocco, Simona; Monasson, Rémi; Schug, Alexander; Weigt, Martin

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.

Zugehörige Institution(en) am KIT Fakultät für Physik (PHYSIK)
Steinbuch Centre for Computing (SCC)
Publikationstyp Zeitschriftenaufsatz
Jahr 2015
Sprache Englisch
Identifikator ISSN: 0305-1048
KITopen ID: 1000051413
HGF-Programm 46.11.01; LK 01
Erschienen in Nucleic Acids Research
Band 43
Heft 21
Seiten 10444-10455
Bemerkung zur Veröffentlichung Gefördert durch den KIT-Publikationsfonds
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