Predicted aligned error (PAE) is a measurement calculated by protein structure prediction neural networks to capture positional errors between two amino acids in a computational model. It was introduced by AlphaFold2. A derivative metric, ipSAE, has been shown to be more robust at identifying potential binders.
Figure from (1)
1.
Chow A, Chu H, Li R, Nalbant BN, Dozic AV, Kida LC, et al. Sequence and structural determinants of efficacious de novo chimeric antigen receptors. openRxiv; 2025. Available from: https://doi.org/10.64898/2025.12.12.694033