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Re: [modeller_usage] Need help with automating Modeller flow?

Ashika Umanga Umagiliya wrote:
> I went through the Basic modeling tutorial
> (http://salilab.org/modeller/tutorial/basic.html) and have several
> questions :
> 1) After step 1 (build_profile.py) we have to select suitable templates
> ,does the selection criteria is e-value =0 ?

You want to pick templates with small E values, so yes, the closer to
zero the better.

> 2) After executing 'compare.py' ,we have to select one pdb template from
> distance matrix?

No, you could build your model using a multiple-template alignment,
particularly if different templates cover different parts of your model
sequence. Or you could repeat the modeling process for each of the
templates, and then pick the best model(s).

> How to implement this in selection logic? What criteria does 'ModWeb'
> application use? Is there any tools to select the best template using
> the distance matrix?

ModWeb selects suitable templates using regular sequence-sequence
searches (which you used in the basic modeling tutorial) as well as
profile-sequence and profile-profile searches, which are often more
sensitive at low sequence identity. These are not covered in the basic
tutorial, but also utilize profile.build() or (PSI-BLAST profiles) and
profile.scan(). Models are then built, and the best selected on the
basis of model assessment scores, such as GA341 and DOPE.

You can also check the CASP pages for ideas. While many groups and
servers use Modeller to build models, there are a range of methods used
to select templates and assess the results.

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage