catRAPID: large-scale sequence-based prediction of protein–RNA interactions

catRAPID estimates the binding propensity of protein-RNA pairs by using sequence information only. The algorithm can be used to predict protein associations with coding and non-coding transcripts. Predictions have proved very accurate (> 0.8) when validated by traditional Immunoprecipitation methods, like RIP and CLIP.

Applications and Services:

• Identifies ‘druggable’ targets in compound libraries targeting protein–RNA interactions;
• Measures Protein-RNA interaction propensity;
• Measures Protein-RNA interaction specificity;
• Predicts protein-binding regions in RNA sequences;
• Predicts of RNA-binding regions in protein sequences ;
• Offers pre-compiled protein-RNA pairs libraries for model organisms;
• Allows generation of custom libraries for large-scale calculations.

Advantages:

• Experimental design: instead of pulling-down a protein and quantifying transcripts with high-throughput sequencing, catRAPID allows to perform  fast in silico screening for identification of potential candidates.  Compared to current approaches (e.g. CLIP), our method dramatically simplifies the workflow, as only a few genes would need to be experimentally validated by real-time PCR.
• Protein and RNA engineering: catRAPID can be used to characterize regions amenable for molecular engineering, as it predicts the binding sites of both protein and RNA molecules. In particular,  for generation of RNA aptamers, catRAPID is dramatically faster, cheaper and more efficient than current approaches (e.g. SELEX), as only few candidates should be synthesized.
• The discovery of protein-RNA interactions can be useful in broad areas of investigation, including stem cells reprogramming and re-wiring of ribonucleoprotein networks involved in viral infection.

Features:

• catRAPID fragments: Divides polypeptide and nucleotide sequences into fragments and predicts their interaction propensities
• catRAPID strength: Computes the strength of a protein-RNA pair with respect to a reference set
• catRAPID omics: Computes the interaction between a molecule (protein/transcript) and the reference set (transcriptome/nucleotide-binding proteome) of a model organism.
• catRAPID express: catRAPID 'express' and catRAPID 'express' omics allow the identification of co-expressed protein and RNA pairs in human tissues.
• catRAPID signature: Searches for RNA-binding regions in protein sequences

External Link:       

http://www.tartaglialab.com/

Closed Source

Available for Licensing and Services