catRAPID

catRAPID predicts protein-RNA interactions and enables proteomic and transcriptomic-scale analyses by estimating binding propensities to identify ribonucleoprotein associations.

Key Features:

• Omics-Level Predictions: Performs proteomic and transcriptomic level predictions to analyze protein-RNA interactions on a genome-wide scale.
• Unrestricted Sequence Analysis: Accepts protein and RNA sequences without size limitations to accommodate large datasets.
• Nucleic Acid Binding Region Identification: Identifies specific protein regions likely involved in nucleic acid binding to inform functional domain analysis.
• RNA Motif Detection: Detects RNA motifs implicated in protein recognition.
• Species Coverage and Custom Libraries: Supports calculations for Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, and Xenopus tropicalis, and allows generation of custom libraries.

Scientific Applications:

• Benchmarking: Validated against known RNA interactomes of SRSF1, EZH2, TDP43, and FUS, and protein interactomes associated with U1/U2 small nucleolar RNAs, Xist RepA region, and CRB3 3'-UTR RNAs, with predictions showing significance (P < 0.05).
• Experimental Prioritization: Prioritizes candidate protein-RNA interactions for experimental validation.

Methodology:

catRAPID estimates binding propensities by integrating secondary structure information, hydrogen bonding, and van der Waals forces.