RBPDB: a database of RNA-binding specificities

The RNA-Binding Protein DataBase (RBPDB) is a collection of experimental observations of RNA-binding sites, both in vitro and in vivo, manually curated from primary literature. To build RBPDB, we performed a literature search for experimental binding data for all RNA-binding proteins (RBPs) with kno...

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Bibliographic Details
Published in:Nucleic acids research 2011-01, Vol.39 (Database issue), p.D301-D308
Main Authors: Cook, Kate B, Kazan, Hilal, Zuberi, Khalid, Morris, Quaid, Hughes, Timothy R
Format: Article
Language:English
Subjects:
Animals
Binding Sites
Caenorhabditis elegans Proteins - chemistry
Caenorhabditis elegans Proteins - metabolism
Databases, Protein
Drosophila Proteins - chemistry
Drosophila Proteins - metabolism
Humans
Metazoa
Mice
Protein Structure, Tertiary
RNA, Messenger - chemistry
RNA, Messenger - metabolism
RNA-Binding Proteins - chemistry
RNA-Binding Proteins - metabolism
Sequence Analysis, RNA
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Description
Summary:The RNA-Binding Protein DataBase (RBPDB) is a collection of experimental observations of RNA-binding sites, both in vitro and in vivo, manually curated from primary literature. To build RBPDB, we performed a literature search for experimental binding data for all RNA-binding proteins (RBPs) with known RNA-binding domains in four metazoan species (human, mouse, fly and worm). In total, RPBDB contains binding data on 272 RBPs, including 71 that have motifs in position weight matrix format, and 36 sets of sequences of in vivo-bound transcripts from immunoprecipitation experiments. The database is accessible by a web interface which allows browsing by domain or by organism, searching and export of records, and bulk data downloads. Users can also use RBPDB to scan sequences for RBP-binding sites. RBPDB is freely available, without registration at http://rbpdb.ccbr.utoronto.ca/.
ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkq1069