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

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...

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Detalles Bibliográficos
Autores principales: De Leonardis, Eleonora, Lutz, Benjamin, Ratz, Sebastian, Cocco, Simona, Monasson, Rémi, Schug, Alexander, Weigt, Martin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2015
Materias:
RNA
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666395/
https://www.ncbi.nlm.nih.gov/pubmed/26420827
http://dx.doi.org/10.1093/nar/gkv932
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author De Leonardis, Eleonora
Lutz, Benjamin
Ratz, Sebastian
Cocco, Simona
Monasson, Rémi
Schug, Alexander
Weigt, Martin
author_facet De Leonardis, Eleonora
Lutz, Benjamin
Ratz, Sebastian
Cocco, Simona
Monasson, Rémi
Schug, Alexander
Weigt, Martin
author_sort De Leonardis, Eleonora
collection PubMed
description 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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spelling pubmed-46663952015-12-02 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 Nucleic Acids Res RNA 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. Oxford University Press 2015-12-02 2015-09-29 /pmc/articles/PMC4666395/ /pubmed/26420827 http://dx.doi.org/10.1093/nar/gkv932 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle RNA
De Leonardis, Eleonora
Lutz, Benjamin
Ratz, Sebastian
Cocco, Simona
Monasson, Rémi
Schug, Alexander
Weigt, Martin
Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction
title Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction
title_full Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction
title_fullStr Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction
title_full_unstemmed Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction
title_short Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction
title_sort direct-coupling analysis of nucleotide coevolution facilitates rna secondary and tertiary structure prediction
topic RNA
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666395/
https://www.ncbi.nlm.nih.gov/pubmed/26420827
http://dx.doi.org/10.1093/nar/gkv932
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