I am building a GPCR homology model and am not sure what template to use. What is the best choice?

This is a difficult question as the sequence similarity will generally be quite low, even for sequences in the same subfamily. There general rule of thumb is to use the template that contains the ligand that is closest in size to your own target ligand and is expected to have a similar binding mode.

Keywords: GPCR, Prime, Homology Modeling, template, similarity

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