Computational Biology: How to find the binding partners?

HI

Do you have a specific protein in mind? Let us know.

my protein is ACBP which is DBI in human.
I will walk through the process in which I reached the entery in pdb.org

First I selected a isofrom that I want to analyze. Got the protein sequece for it and used Blast again (protein data base) from which I got the conserved domains for the gene. I chose the broadest domain and from which I got two pdb id numbers:


for your reference:
http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?ascbin=8&maxaln=10&seltype=2&uid=238248

Now I got the acyl-CoA and CoA, which I suppose are the two different binding sites.. I think I am supposed to get three.

Then I visualize them using JMol. Are those:"acyl-CoA and CoA" the binding sites?

1) http://www.ebi.ac.uk/interpro/entry/IPR000582

2) http://europepmc.org/abstract/MED/11491287