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Table 6 Topological measures to discriminate between native and decoy sets - a case study on the cyclophilin-like fold

From: Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs

Category Similarity (snet) Distance (dnet)
  Mean Min Max Mean Min Max
Random
Sequences
0.156
(0.093)
0.032 0.452 0.880
(0.081)
0.650 1.000
Sequences from other folds 0.143 (0.097) 0.000 0.387 0.880 (0.079) 0.676 1.000
2HAQ 0.405 (0.089) 0.129 0.677 0.688 (0.069) 0.486 0.909
3BO7_B 0.390 (0.081) 0.194 0.613 0.734 (0.060) 0.558 0.880
3KOP_F 0.307 (0.063) 0.032 0.484 0.766 (0.049) 0.639 0.969
  1. 250 files from each category, two decoy sets and three sequences native to the cyclophilin-like fold were used in the calculations. For all sequences, side chain conformers were assigned randomly. 3BO7_B and 3KOP_F has 37% and 11% sequence identity to 2HAQ. Standard deviation for each measure is given in parenthesis.