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, but depends on seqID and so this can't be used (i don't think?) on threaded models. DOPE can be, and normalized zDOPE seems recommended for comparison of models from different homologues.
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?
beyond the main CASP results, does anyone else have experience trying to compare threaded vs. homologue models in terms of these metrics, or others? thanks for any leads,
rik