Figure 7

Flowchart of the four-step docking procedure used in this work. Peptides are docked into DRB1*0402 using a four-step procedure consisting of: (i) pseudo-Brownian rigid body docking of peptide fragments to the ends of the binding groove, (ii) central loop closure by satisfaction of spatial constraints, (iii) refinement of the backbone and side-chain atoms of the core recognition residues and receptor contact regions and (iv) extension of flanking peptide residues by satisfaction of spatial constraints.