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.

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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.”

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