Hi,

you can try any software that predicts pockets/cavities. I would suggest fpocket because it also gives you a "druggability" score.

CASTp (http://sts.bioe.uic.edu/castp/index.html?201l) will give you the probable pocket of a protein

Mayur Mukhi I have installed the CASTp plugin inside PyMol but it is not taking .pdb files as an input and is flagging the following error:

OSError: [Errno 22] Invalid argument

You could try using the web server. Somone may have already used it for your protein. This kind of information is usually stored in the web server

Mayur Mukhi I uploaded the protein in the calculations tab on the link you provided but it says: Cannot access the server. Please try again later.

In that case, you could try MetaPocket (https://projects.biotec.tu-dresden.de/metapocket/algorithm.php).

What is the PDB ID of your protein?

Ok, I will try MetaPocket. Thanks for the guidance.

Discovery Studio can predict the potential binding site based on protein cavities.

Receptor-Ligand Interactions>Define and Edit Binding Site>From Receptor Cavities