RBPDB: a database of RNA-binding specificities

By Kate B. Cook, Hilal Kazan, K. Zuberi, Quaid Morris, T. Hughes. Nucleic Acids Res., 2010

581 citations recorded by the source corpus.

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/.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e70622a35880b552e12d664d5bf55eaa55f189df

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Citations in the corpus

Revealing protein–lncRNA interaction (2015, unknown): “RBPDB [53] is a database of binding determinants for a collection of RBPs, some of which can bind lncRNAs.”
RBPmap: a web server for mapping binding sites of RNA-binding proteins (2014, unknown): “Given the preferred binding sequences for a given RBP, several computational tools are currently available for mapping the motifs on a query sequence (18,20,22,29,30).”
A census of human RNA-binding proteins (2014, unknown): “, 2013), and the RBPDB database of human RBPs with canonical RBDs (Cook et al., 2011) (red).”
High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorder (2015, methodology): “We compared our predictions against the known DNA and RNA-binding proteins in these proteomes that were annotated based on several large databases including gene ontology (GO) terms (53) in UniProt, RBPDB (54) for the RNA-binding proteins, and animalTFDB (55) for the DNA-binding proteins.”
Fragile X Mental Retardation Protein: A Paradigm for Translational Control by RNA-Binding Proteins (2015, unknown): “There are more than 400 RNA-binding proteins (RBP) encoded in the human genome and they regulate diverse processes such as mRNA transcription, splicing, polyadenylation, transport, translation, and RNA degradation (Cook et al., 2011).”
Predicting RNA-Protein Interactions Using Only Sequence Information (2011, methodology): “Currently, two basic types of information regarding RNA-protein interaction partners are widely available: i) experimentally-deter-mined structures of RNA-protein complexes, available in primary resources such as the PDB [26] and NDB [41], and secondary resources such as PRIDB [34] and BIPA [42]; an”