Predicted Aligned Error
The Predicted Aligned Error (PAE) is a quantitative output produced by AlphaFold, a protein structure prediction system developed by DeepMind, and other similar programs. During training, the aligned error between two residues, i and j is calculated by aligning the predicted N, Cα, and C atoms of residue i onto the same atoms in the experimental structure in the training data, and measuring the resulting distance between the predicted position of the Cα atom of residue j and the experimental position of that atom.