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.