Structural Characterization of RNA-Binding Sites of Proteins: Preliminary Results

dc.contributor.author Towfic, Fadi
dc.contributor.author Gemperline, David
dc.contributor.author Caragea, Cornelia
dc.contributor.author Wu, Feihong
dc.contributor.author Dobbs, Drena
dc.contributor.author Dobbs, Drena
dc.contributor.author Honavar, Vasant
dc.contributor.department Computer Science
dc.contributor.department Genetics, Development and Cell Biology
dc.contributor.department Bioinformatics and Computational Biology
dc.date 2018-02-18T05:09:04.000
dc.date.accessioned 2020-06-30T04:00:52Z
dc.date.available 2020-06-30T04:00:52Z
dc.date.copyright Mon Jan 01 00:00:00 UTC 2007
dc.date.embargo 2017-03-02
dc.date.issued 2007-01-01
dc.description.abstract <p>We explore whether protein-RNA interfaces differ from non-interfaces in terms of their structural features and whether structural features vary according to the type of the bound RNA (e.g., mRNA, siRNA...etc.), using a nonredundant dataset of 147 protein chains extracted from protein-RNA complexes in the protein data bank. Our analysis of surface roughness, solid angle and CX value of amino acid residues for each of the protein chains in the dataset shows that: The protein-RNA interface residues tend to be protruding compared to non-interface residues and tend to have higher surface roughness and exhibit moderately convex or concave solid angles. Furthermore, the protein chains in protein-RNA interfaces that contain Viral RNA and rRNA significantly differ from those that contain dsRNA, mRNA siRNA, snRNA, SRP RNA and tRNA with respect to their CX values. The results of this analysis suggests the possibility of using such structural features to reliably identify protein-RNA interface residues when the structure of the protein is available but the structures of complexes formed by the protein with RNA are not.</p>
dc.description.comments <p>This is a proceeding from <em>IEEE International Conference on Bioinformatics and Biomedicine Workshops </em>(2007): 60-66, doi: <a href="https://doi.org/10.1109/BIBMW.2007.4425401" target="_blank">10.1109/BIBMW.2007.4425401</a>. Posted with permission.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/gdcb_las_conf/10/
dc.identifier.articleid 1009
dc.identifier.contextkey 9780787
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath gdcb_las_conf/10
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/37741
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/gdcb_las_conf/10/ms2007_Dobbs_StructuralCharacterization.pdf|||Fri Jan 14 18:08:00 UTC 2022
dc.source.uri 10.1109/BIBMW.2007.4425401
dc.subject.disciplines Bioinformatics
dc.subject.disciplines Cell and Developmental Biology
dc.subject.disciplines Computational Biology
dc.subject.disciplines Genetics and Genomics
dc.title Structural Characterization of RNA-Binding Sites of Proteins: Preliminary Results
dc.type article
dc.type.genre conference
dspace.entity.type Publication
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