RBPDB

RNA-Binding Protein DataBase (RBPDB): Curated repository of experimental RNA-binding site data

RNA-Binding Protein DataBase (RBPDB) compiles experimentally validated RNA-binding sites for RNA-binding proteins (RBPs) with known RNA-binding domains in human, mouse, fly, and worm. The database contains curated binding data for 272 RBPs derived from primary literature, including in vitro and in vivo observations.

Key Features:

• Manual Literature Curation: Integrates experimentally validated RNA-binding data extracted from primary publications.
• Position Weight Matrix Motifs: Provides position weight matrix (PWM) motifs for 71 RBPs.
• In Vivo Binding Data: Includes sequences of in vivo-bound transcripts identified by immunoprecipitation experiments for 36 RBP datasets.
• Sequence Scanning: Enables computational scanning of input sequences to identify potential RBP-binding sites.

Scientific Applications:

• Post-Transcriptional Gene Regulation Analysis: Supports investigation of RNA–protein interactions, RBP binding specificity, and regulatory mechanisms across metazoan species.
• Disease Mechanism Studies: Facilitates analysis of dysfunctional RBPs and their roles in human disease.

Methodology:

Aggregates RNA-binding site data through systematic literature review and manual curation, annotating RBPs with known RNA-binding domains. Stores experimentally derived binding sequences and position weight matrix motifs, and applies motif-based sequence scanning to predict candidate RBP-binding sites.