Skip to main content

Table 7 Comparison of methods for substructure searching.

From: Tableau-based protein substructure search using quadratic programming

Fold SCOP sid P S T Q R P/R S/R T/R Q/R
β-grasp d1ubia_ 33 9 42 14 15 15/15 9/15 13/15 10/15
Key-barrel d1tttb1 10 3 0 17 5 5/5 1/5 0/5 4/5
Immunoglobulin d1ae6h1 27 1 4 1 11 9/11 1/11 4/11 1/11
Plait (ferredoxin) d1bhne_ 20 1 61 14 28 7/28 1/28 24/28 6/28
GFP-like d1h6rb_ 1 1 58 21 1 1/1 1/1 1/1 1/1
Jelly-roll d2phlb1 1 1 19 15 12 1/12 1/12 10/12 5/12
TIM-barrel d1tima_ 16 16 40 33 32 16/32 16/32 28/32 32/32
NAD-binding fold d1f6dc_ 1 1 42 19 8 1/8 1/8 7/8 5/8
  1. The number of superfamilies in the ASTRAL SCOP 95% sequence identity nonredundant database found for the eight query structures by ProSMoS (P), SSM (S), TOPS (T) and our method, QP tableau search (Q). ProSMoS and SSM return a list of significant hits, so the number of superfamilies found by these hits is shown. Other methods return scores for all database structures, and the number of superfamilies in the hits with a Z-score ≥ 3.0 are shown. The R column is the number of superfamilies, from the combined list of those found by all methods, 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 found by the specified method.