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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Theresa Hsu Sent: Friday, 23 May 2014 7:49 a.m. To: CCP4BB@JISCMAIL.AC.UK 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
