Maggie,
We have developed GPCRModSim, a web server that facilitates the process of
modeling GPCRs using Modeller as a back end modeling tool (
http://gpcr.usc.es).
In particular, once you upload your sequence or swissprot code, you will get
an optimized alignment with all crystallized GPCRs (you can choose also
between templates in the active or inactive conformations). The server will
recommend you the most suitable template based on TM homologies, although
you can further inspect this and change the default selection on the basis
of homologies between particular regions.
Please visit http://gpcr.usc.es
For a test case, the H1 histamine receptor modeled with excelent accuracy,
see the tutorial at http://gpcr.usc.es/tutorial
There are several other features, like the possibility of loop refinement
(using loopmodel routines) and the MD simulation of your simulated model in
an atomistic model of the membrane (using GROMACS routines).
Hugo
--
Hugo G. de Teran, PhD.
"Parga Pondal" Research fellow
Fundación Pública Galega de Medicina Xenómica - SERGAS
Santiago de Compostela (SPAIN)
Phone +34 881813873
e-mail:hugo.teran@usc.es
http://webspersoais.usc.es/hugo.teran
2011/10/18 Maggie Pruitt
mamdahl@iastate.edu
> 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
>
> _______________________________________________
> modeller_usage mailing list
> modeller_usage@salilab.org
>
https://salilab.org/mailman/listinfo/modeller_usage
>
>
--
--
Hugo G. de Teran, PhD.
"Parga Pondal" Research fellow
Fundación Pública Galega de Medicina Xenómica - SERGAS
Santiago de Compostela (SPAIN)
Phone +34 881813873
e-mail:hugo.teran@usc.es
http://webspersoais.usc.es/hugo.teran
--
--
Hugo G. de Teran, PhD.
"Parga Pondal" Research fellow
Fundación Pública Galega de Medicina Xenómica - SERGAS
Santiago de Compostela (SPAIN)
Phone +34 881813873
e-mail:hugo.teran@usc.es
http://webspersoais.usc.es/hugo.teran
Hugo Gutierrez de Teran