AlphaFold model quality self-assessment improvement via deep graph learning.

Abstract

In recent years, significant advancements have been made in deep learning-based computational modeling of proteins, with DeepMind's AlphaFold2 standing out as a landmark achievement. These computationally modeled protein structures not only provide atomic coordinates but also include self-confidence metrics to assess the relative quality of the modeling, either for individual residues or the entire protein. However, these self-confidence scores are not always reliable; for instance, poorly modeled regions of a protein may sometimes be assigned high confidence. To address this limitation, we introduce Equivariant Quality Assessment Folding (EQAFold), an enhanced framework that refines the Local Distance Difference Test prediction head of AlphaFold to generate more accurate self-confidence scores. Our results demonstrate that EQAFold outperforms the standard AlphaFold architecture and recent model quality assessment protocols in providing more reliable confidence metrics. Source code for EQAFold is available at https://github.com/kiharalab/EQAFold_public.