Hello,
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.
If anyone can give me some further insight on this manner, I would greatly appreciate it.
Thanks in advance for your help!
Sincerely,
Maggie
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
participants (2)
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Maggie Pruitt -
Modeller Caretaker