Hi,

I have used the catRAPID prediction algorithm, with a global score analysis for long RNA transcripts.

Dear Rohit,

First you need to generate a 3D structure of the protein of interest using Comparative modeling (Modeler - if you have a known homologous 3D structure available in PDB) or Ab Initio modeling using I - Tasser server. Following this you need to check for model quality using RAMPAGE (Basic Ramachandran Plot analyses) and QMEANS (structure quality assessment)

Once you have done that you can then analyse the Protein binding sites on your transcript of interest using "iDeepE [https://github.com/xypan1232/iDeepE.]

Following this you can design the 3D structure of your RNA using RNA Composer (500nt) servers;

So at this point you would have a 3D protein structure and a 3D RNA structure. You can then dock these two files using NPDOCK server to evaluate the binding residues. Alternatively you can also use GOLD for docking.

All the above programs have excellent manuals and help pages for support.

Hope this helps

Best Wishes

S.G.