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DeepCLIP: Predicting the effect of mutations on protein-RNA binding with Deep Learning

biorxiv. 2019; 
Alexander Gulliver Bjørnholt Grønning, Thomas Koed Doktor, Simon Jonas Larsen, Ulrika Simone Spangsberg Petersen, Lise Lolle Holm, Gitte Hoffmann Bruun, Michael Birkerod Hansen, Anne-Mette Hartung, Jan Baumbach, Brage Storstein Andresen
Products/Services Used Details Operation
Custom DNA/RNA Oligos Surface plasmon resonance imaging (SPRi) by IBIS MX-96 was used to measure the kinetics of recombinant hnRNP A1 (ab224866, Abcam), SRSF1 (GenScript, Piscataway, NJ, USA) and TDP-43 (R&Dsystems, AP-190) binding to the immobilized RNA oligonucleotides. Get A Quote

摘要

Nucleotide variants can cause functional changes by altering protein-RNA binding in various ways that are not easy to predict. This can affect processes such as splicing, nuclear shuttling, and stability of the transcript. Therefore, correct modelling of protein-RNA binding is critical when predicting the effects of sequence variations. Many RNA-binding proteins recognize a diverse set of motifs and binding is typically also dependent on the genomic context, making this task particularly challenging. Here, we present DeepCLIP, the first method for context-aware modeling and predicting protein binding to nucleic acids using exclusively sequence data as input. We show that DeepCLIP outperforms existing methods fo... More

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