Confidence Metrics
AlphaFold uses two confidence metrics: PAE and pLDDT.
PAE: Predicted Aligned Error
PAE is the expected position error at residue X when predicted and true structures are aligned on residue Y.
pLDDT: Predicted Local Distance Difference Test
pLDDT is a per-residue confidence score (0–100). It is a “superposition-free score that evaluates local distance differences of all atoms in a model, including validation of stereochemical plausibility.”