Hi Theresa,
I tackled a similar problem recently using modeller (Andrej Sali) which worked well. In the case of my transporter (or any model) your homology model will only be as good as the starting structure (resolution etc) and your sequence identity. I found that the homologues that I was looking at were simply too distant from the human transporter to actually be of any use.
Hope this helps
Joel
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Theresa Hsu
Sent: Friday, 23 May 2014 7:49 a.m.
To: [log in to unmask]
Subject: [ccp4bb] Off topic: Homology modeling
Dear all
I am working with a membrane protein without known structure. The closest protein in PDB has 10% sequence identity/25% similarity to my protein.
What is the best method and software to do homology modeling while I try to get the crystal? Is the ligand binding site prediction reliable? There is no available experimental data on this protein except to sugest it is some type of ion transport.
Thank you.
Theresa
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