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

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!

protein binding domain rna
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updated by Mensur Dlakic Mensur Dlakic • written by noahhelton98 • noahhelton98

1 answer

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.

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written by Mensur Dlakic Mensur Dlakic

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

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written by noahhelton98 • noahhelton98

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