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Re: [modeller_usage] model quality: GA341, DOPE and zDOPE

On 03/29/2012 11:02 AM, richard k belew wrote:

i'm trying to evaluate models generated by Modeller in comparison
to some built using threading methods (ITasser).  GA341 seems the
primary coin-of-realm in Modeller-land
Maybe 5 years ago... the newer DOPE method is superior. See Protein Sci 17, 1881-1893, 2008 (#205 at http://salilab.org/publications/) 


but in trying to compare models, i'm finding Modeller
models that have excellent (>  0.8) GA341 scores but
pretty terrible (1 - 1.5) zDOPE scores.  and so in comparison
to ITasser models with good zDOPE scores (~ -0.5), these
threaded models would seem preferred?
I would trust zDOPE over GA341. But neither zDOPE nor GA341 cares whether the model is generated by Modeller or by some other method - they simply take PDBs as input. 

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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