Extended Data Fig. 7: Conformational clustering of the Trp6 sidechain from the MD simulations of the neoepitope and WT peptide-HLA-A*02:06 complexes.
From: Structural dissimilarity from self drives neoepitope escape from immune tolerance
a, Conformations of the five most populated clusters in both simulations. These five accounted for >99% of the conformations sampled in both simulations. Cluster 1 (orange) matches the binding-competent conformation and cluster 4 (green) matches the WT conformation as shown in Figs. 1 and 3 and defined in Fig. 4. b, Total occupancy of the clusters in the two simulations. c, Time resolved charts of the occupancy of clusters. Each simulation enters and exits the binding competent conformation (cluster 1) multiple times, indicating that the greater occupancy of cluster 1 in the neoepitope simulation is not the result of a simulation trapped in a local minimum.
