Peptide sequences determined by molecular modeling.

All docked peptide structures were subjected to the redesign protocol. Shown below are representative redesigned sequences from different peptide backbone conformations (1-ns, 9-ns, or 10-ns) and from different binding sites. The peptide A1M (CLDGGGKGC) exhibited both a high binding mode rank and a low ΔΔG value; thus we select it for experimental testing. aBinding mode rank pertains to the order of the cluster size to which the peptide complex belongs. A binding mode of rank 1 implies that the peptide is positioned on the site to which most other structures are also docked. bM2 and M3 come from different binding sites but with equal number of docked peptides.