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Re: [modeller_usage] Modeling GPCRs



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
--
             http://www.salilab.org/modeller/
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