Prediction of RNA binding regions in protein

Question

[EagleEye]

Hello everyone,

I have a set of proteins (amino acid sequence, structure not know and no homologue secondary structure) where I need to look for binding sites for particular RNA/noncoding (nucleotide sequence).

Things done: I got potential RNA binding regions in protein using RNABindRPlus.

Things need to be done: I have RNA and have to check which part of RNA fragments are binding to the predicted RNA binding sites in the protein.

May be the approach I have taken is wrong all together (I am completely new to this kind of analysis). Please suggest me some methods/approaches to solve this.

[Jean-Karim Heriche]

Have a look at the tools in the protein-RNA interaction category on omictools.com. There may be one you could use.

[EagleEye]

Finally I got a reply. Thanks a lot for your kind reply. I will look into the list.