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