Re: [modeller_usage] Regarding Best Selection of model decoy

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 02/13/2010 03:12 AM, Ashish Runthala wrote:
> How do i consider the following analysis during the modeler run
> itself  like assess.dope, assess.GA341 etc in model-mult.py etc.
> 1. Z score as Modeler doesn't reach below 1 in z scores.

Normalized DOPE Z scores are typically the most reliable method of model 
assessment.

> 2. RMSD to the template structure with just one template considered.

This doesn't make a whole lot of sense, since Modeller always builds 
models that are structurally similar to the template. This will simply 
give you a score that strongly correlates with the sequence identity.

> 3. GDT-TS scores etc.

Sure, if you have the known (native) structure, one benchmark is to 
compare the model against the native using the GDT-TS score.

You can add additional assessment methods to automodel by simply writing 
a Python function and adding that Python function to the assess_methods 
list in the automodel constructor. For example, the GA341 assessment 
method simply looks like:

def GA341(atmsel):
    """Returns the GA341 score of the given model."""
    mdl = atmsel.get_model()
    return ('GA341 score', mdl.assess_ga341())

> And to modeler caretaker, i have something to share with you. How to
> go about that.

You can find contact details on our website:
http://salilab.org/modeller/contact.html

	Ben Webb, Modeller Caretaker
--
modeller-care@ucsf.edu             http://www.salilab.org/modeller/
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