Re: [modeller_usage] Modeling GPCRs

[Modeller Caretaker <>]

On 10/18/11 1:57 PM, Maggie Pruitt wrote:
> I am interested in using Modeller for predicting the structure of the G
> protein-coupled receptor I study. This protein does not have any
> homologous proteins in the PDB database and there is no experimental
> data to help model the protein. Knowing this, can Modeller provide an
> accurate structure of my protein to use in molecular dynamics
> simulations? I understand that I can choose other crystallized GPCRs to
> use as templates, but I am concerned that since Modeller is a homology
> modeling program that the end model would simply look like my protein
> forced onto the template structure.

Yes, you are exactly correct. Modeller is not limited to using homologs 
as templates; it can use any protein that you believe is structurally 
similar to the protein you intend to model. But if you choose a template 
that is not similar, you will likely get a poor model.

	Ben Webb, Modeller Caretaker
--
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