Dear Modeller users,
I have generated some models using Modeller, and I wonder if you could recommend the best way to evaluate them. My sequence homology between modeled protein and the templates is about 30%, so the confidence in some regions of the sequence alignments is low.
I have generated several plots for energy versus residue number using ProsaII, and these show quite nicely which regions have poorer structure. These correlate to regions of low sequence conservation in the alignments.
My question to you is how valid the more specific analyses of atomic-level contacts in the models would be. I have run Procheck and Whatif analyses as well, and the quality check scores are within acceptable ranges. In cases with 30% homology I would expect many errors in atom placements, so should I even consider these stereochemical and packing constraints?
Can you recommend a good reference that discusses these issues?
Thanks very much for your help.
Giselle Knudsen graduate student, CCB Program University of California San Francisco firstname.lastname@example.org