Figure 6.

MASTER-based loop remodeling exercise. (A) Helical and strand segments shown in magenta and cyan, respectively, are used together as a query motif to rebuild the loop between them. Shown in gray are loop geometries from the top 100 matches (all under 0.5 Å full-backbone RMSD; five matches with different loop lengths were omitted for clarity; matches were fused with the query as detailed in Materials and Methods section). The inset shows a sequence logo diagram emergent from the sequences of these matches. (B) Fraction of two-residue loop matches as a function of full-backbone RMSD cutoff. The inset shows the distribution of loop lengths up to 20 residues for the least stringent cutoff. Two-residue loops still dominate, though other possibilities exist (e.g., seven-residue loops).