Figure 4

Structural comparison of the lowest energy docked conformations and the experimental structures of the bound peptide for the pMHC structure 2gtw when the formic acid molecule was a. omitted and b. included in the docking simulation. The peptides are shown in stick representation of all heavy atoms. The Cα RMSD values between the lowest energy predicted (green) and the native conformation of the cognate peptide (blue) for the structure 2gtw when the formic acid molecule was omitted and included in the docking protocol were 3.08 Å and 0.24 Å respectively. The peptide residues of its native conformation that were not accurately docked in the absence of the formic acid molecule are labeled in black in (a). The formic acid molecule is depicted in red in (b).