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Table 8 Comparison of the unique hits from each method for substructure searching.

From: Tableau-based protein substructure search using quadratic programming

Fold SCOP sid Pu Su Tu Qu R Pu/R Su/R Tu/R Qu/R
β-grasp d1ubia_ 17 0 27 4 1 1/1 0/1 0/1 0/1
Key-barrel d1tttb1 4 0 0 10 1 1/1 0/1 0/1 0/1
Immunoglobulin d1ae6h1 25 0 2 0 9 7/9 0/9 2/9 0/9
Plait (ferredoxin) d1bhne_ 8 0 48 7 21 1/21 0/21 17/21 3/21
GFP-like d1h6rb_ 0 0 56 19 0 0/0 0/0 0/0 0/0
Jelly-roll d2phlb1 0 0 15 11 9 0/9 0/9 7/9 2/9
TIM-barrel d1tima_ 0 0 11 3 3 0/3 0/3 0/3 3/3
NAD-binding fold d1f6dc_ 0 0 33 10 4 0/4 0/4 3/4 1/4
  1. The number of superfamilies in the ASTRAL SCOP 95% sequence identity nonredundant database found by only that method for the eight query structures by ProSMoS (Pu), SSM (Su), TOPS (Tu) and our method, QP tableau search (Qu). The R column is the number of superfamilies, from the combined list of those found uniquely by each method, in which the relevant query pattern or fold description is explicitly mentioned in the SCOP structure description. The ratio columns show the number of superfamilies in the R column represented by the superfamilies found only by the specified method.