Figure 1

Pairwise RMSD matrix plot for 1ctf in the 4state_reduced, lattice_ssfit, lmds and semfold decoy sets. Each column or row represents one decoy conformation, and each cell represents the pairwise RMSD between the two conformations that correspond to the row and the column. Both columns and rows are ordered by the C_α RMSD between the corresponding decoy conformation and the experimentally determined conformation. The color of the cells reflects the value of the pairwise RMSD between two decoys: the darker the cell, the lower the pairwise RMSD. The dimension of the four matrices are 630 × 630 (a), 1000 × 1000 (b), 497 × 497 (c) and 1000 × 1000 (d), respectively. Low-RMSD decoy conformations tend to have lower pairwise RMSD with each other.