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Re: [modeller_usage] homology modelling vs protein threading

On 12/19/2009 04:38 AM, Thomas Evangelidis wrote:
I want to build models of ATP-binding domains with sequence identity
ranging between 40% and 50%. In the FAQs it says that one needs 35-40%
at least to build reliable models. However these models will be used for
inhibitor design, therefore the accuracy of the structure prediction
method will determine the outcome. Do you reckon the sequence similarity
is enough to get a good model of the domain, or should I try other
programs based on threading? Is there a way to compare the quality of
the structures derived from these 2 different methodologies?

You can never be sure, of course, and sequence identities are not a reliable predictor of model quality, but at 40-50%, you're quite likely to get good quality models. Most assessment methods (e.g. normalized DOPE, GA341, Prosa) will work just fine on both Modeller-generated models and those generated with threading programs, so you can compare your models that way.

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