This title appears in the Scientific Report :
2020
Please use the identifier:
http://dx.doi.org/10.1261/rna.073809.119 in citations.
Evaluating DCA-based method performances for RNA contact prediction by a well-curated data set
Evaluating DCA-based method performances for RNA contact prediction by a well-curated data set
RNA molecules play many pivotal roles in a cell that are still not fully understood. Any detailed understanding of RNA function requires knowledge of its three-dimensional structure, yet experimental RNA structure resolution remains demanding. Recent advances in sequencing provide unprecedented amou...
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Personal Name(s): | Pucci, Fabrizio (Corresponding author) |
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Zerihun, Mehari B. / Peter, Emanuel K. / Schug, Alexander | |
Contributing Institute: |
Jülich Supercomputing Center; JSC |
Published in: | RNA, 26 (2020) 7, S. 794 - 802 |
Imprint: |
Stanford, Calif.
HighWire Press
2020
|
PubMed ID: |
32276988 |
DOI: |
10.1261/rna.073809.119 |
Document Type: |
Journal Article |
Research Program: |
Doktorand ohne besondere Förderung Forschergruppe Schug Computational Science and Mathematical Methods |
Publikationsportal JuSER |
RNA molecules play many pivotal roles in a cell that are still not fully understood. Any detailed understanding of RNA function requires knowledge of its three-dimensional structure, yet experimental RNA structure resolution remains demanding. Recent advances in sequencing provide unprecedented amounts of sequence data that can be statistically analyzed by methods such as direct coupling analysis (DCA) to determine spatial proximity or contacts of specific nucleic acid pairs, which improve the quality of structure prediction. To quantify this structure prediction improvement, we here present a well curated data set of about 70 RNA structures of high resolution and compare different nucleotide–nucleotide contact prediction methods available in the literature. We observe only minor differences between the performances of the different methods. Moreover, we discuss how robust these predictions are for different contact definitions and how strongly they depend on procedures used to curate and align the families of homologous RNA sequences. |