Figure 2.

Identification of a low Rosetta energy model which closely mimics the crystal structure of a designed permuted variant. A: Plot of Rosetta energy versus rmsd to the crystal structure of 006, for the 2500 models with different loop conformations (blue circles) generated by RosettaRemodel. The 2500 models were clustered by all-against-all rmsd of the designed linkers, and red diamonds show the lowest Rosetta energy models from the three largest clusters. B: The crystal structure of the 006 permuted variant (red) was in close agreement with the lowest energy model from the largest cluster (green). No major changes were observed in terms of the overall fold relative to the original epitope-scaffold. C: Comparison of the linker region in the original epitope-scaffold (magenta) and the permuted version (red). D: Comparison of the linker region in the lowest energy model from the largest cluster (green) and the crystal structure (red). Side-chains are shown in sticks.