Protein structure measurement

pLDDT

"predicted Local Distance Difference Test" is a per-residue measure of local confidence. It is scaled from 0 to 100, with higher scores indicating higher confidence and usually a more accurate prediction. ref

PAE

Predicted Aligned Error (PAE) is a measure of how confident AlphaFold2 is in the relative position of two residues within the predicted structure. PAE is defined as the expected positional error at residue X, measured in Ångströms (Å), if the predicted and actual structures were aligned on residue Y.ref