Benchmarking of AlphaFold2 accuracy self-estimates as indicators of empirical model quality and ranking: a comparison with independent model quality assessment programmes

Despite an increase in protein modelling accuracy following the development of AlphaFold2, there remains an accuracy gap between predicted and observed model quality assessment (MQA) scores. In CASP15, variations in AlphaFold2 model accuracy prediction were noticed for quaternary models of very similar observed quality. In this study, we compare plDDT and pTM to their observed counterparts the local distance difference test (lDDT) and TM-score for both tertiary and quaternary models to examine whether reliability is retained across the scoring range under normal modelling conditions and in situations where AlphaFold2 functionality is customized. We also explore plDDT and pTM ranking accuracy in comparison with the published independent MQA programmes ModFOLD9 and ModFOLDdock.