Figure 3.

Measures for the rankings of all 16 epitope scaffolds for three overlapping four-residue subepitopes of EKTKEQ in α-synuclein (top of each column). (a) Scaffolded cyclic peptide ensemble dissimilarity to monomer (triangle), fibril (star), and stressed fibril (circle) ensembles, as measured by Jensen–Shannon divergence (JSD), showing the changes in ensemble overlap with varying numbers of flanking glycines. (b) Scaffolded cyclic peptide ensemble embedding depth within the monomer (triangle), fibril (star), and stressed fibril (circle) ensembles, showing the changes in ensemble embedding with varying number of flanking glycines. (c) Normalized off-pathway targeting values (OP) for scaffolds with varying number of flanking glycines. Higher values indicate there is less predicted off-pathway targeting by a given scaffold. The ranks of the top 10 scaffolds are indicated in the figure panels, along with the rank for the highest ranking scaffold (15) for epitope KTKE.