Sir Ben is correct. But there is an option to let your model be biased to its actual native state, instead of forcing it to the topology of your templates. Select good templates which you might have already done correctly. Now if you know how to make a correct representative alignment for your target, that is the best choice. Or if you don't try to harness continuous or discontinuous reliable structural folds from templates as per your constraints. Don't rely simply on MD to relax the models. If your first model is distant from its native state, no way you can pull it through. So focus on template selection and correct alignment to build your model through these reliable scaffolds.

Good Luck Ashish

Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

----- Original Message ----- From: "modeller usage-request" modeller_usage-request@salilab.org To: "modeller usage" modeller_usage@salilab.org Sent: Wednesday, October 19, 2011 12:12:24 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 123

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Today's Topics:

1. Re: Modeling GPCRs (Modeller Caretaker) 2. Re: Modeling GPCRs (Hugo Gutierrez de Teran)

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Message: 1 Date: Tue, 18 Oct 2011 17:52:46 -0700 From: Modeller Caretaker modeller-care@salilab.org Subject: Re: [modeller_usage] Modeling GPCRs To: Maggie Pruitt mamdahl@iastate.edu Cc: modeller_usage@salilab.org Message-ID: 4E9E1F5E.8010507@salilab.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed

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