Predicted Aligned Error (PAE)
Tutorial to Generate Predicted Aligned Error (PAE) Plots from AlphaFold Output Files What is PAE? The Predicted Aligned Error (PAE) is a critical output from AlphaFold that estimates the pairwise confidence of residue positions within a predicted protein structure. Unlike pLDDT, which provides confidence scores for individual residues, the PAE matrix gives insight into the relative accuracy between all pairs of residues. This is particularly useful for assessing domain packing, identifying flexible regions, or validating inter-domain orientations in complex proteins. How AlphaFold Produces .pkl Files? When AlphaFold predicts protein structures, it outputs several result files, including .pkl files (e.g., result_model_1_pred_0.pkl ). These files contain a nested dictionary of various data arrays, including: • plddt : Per-residue confidence scores (0–100). • distogram : Pairwise distance probabilities. • predicted_aligned_error : A matrix of pairwise a...