Program for predicting RNA sequences that may bind to a protein Domain

Question

[noahhelton98]

Hi all, I have two RNA recognition motifs (RRMs) that I am interested in for the RBM39 protein. I was wondering if anyone was familiar of any software that might be able to predict potential RNA sequences that would be recognized by these domains. Thanks so much!

Answer 1

[Mensur Dlakic]

I don't think you will be able to find such a tool. To answer your question more broadly, we do not have the ability to predict target sequences for either DNA- or RNA-binding proteins. There are some exceptions when it comes to DNA-binding proteins, for example zinc-finger proteins and TAL effectors. Those we can design in such a way to recognize a particular DNA sequence, but this is not true for all proteins that bind nucleic acids.

[noahhelton98]

Thanks for your answer! Guess I will have to go back to drawing board some. Thank you!