[Chimera-users] Homology modelling with Chimera/Modeller

StaidsonBio yong.yin at staidsonbio.com
Sat Feb 13 14:38:55 PST 2021


I am trying to do homology modelling with Chimera/Modeler for a Fc fusion protein, which contains three domains, one is Fc, one is receptor and the 3rd is ligand. Fc has many PBD structures in PDB database and the receptor has couple of 3D structures with the ligand as well. I used the fusion protein sequence to do blast in Chimera and it gave matched sequence files to Fc domain only, no sequence files for the receptor-ligand complex, even it already has couple of solved 3D crystal structure files in PDB database. Is there any suggestion about this issue? Can I do separately, use Fc domain alone as search sequence for its template and use receptor-ligand sequences as search sequence for its template? If it is ok, there are two template files. How to make them into one template file for modelling late?

Thanks very much for your suggestion.



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