Figure 3

Comparison of the lowest energy predicted and the experimental structures of the cognate peptides with the least RMSD values across the pDOCK test set. a. KAVYNFATM peptide in the MHC-I complex 1s7q (PDB code). b. XXRXXX peptide in the MHC-II complex 1d5x (PDB code). The peptides are shown in stick representation of all heavy atoms. The Cα RMSD values between the lowest energy docked conformation (green) and the native conformation of the bound peptides (blue) for the MHC-I structure 1s7q (PDB code) and the MHC-II structure 1d5x (PDB code) are 0.09 Å and 0.11 Å, respectively. X: Amino acid analogues (chemical mimics).