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Table 8 Comparison between SA-FAST, 3D-BLAST, PSI-BLAST, YAKUSA, MAMMOTH, and CE on 50 proteins selected from SCOP95-1.69

From: Protein structure search and local structure characterization

Search tool Average time required for a query (sec) Relative to SA-FAST Accuracya (%) Average precisionb (%)
SA-FAST 1.15 1.00 96 90.80
3D-BLAST 1.30 1.13 94 85.20
PSI-BLAST 0.48 0.42 84 68.16
YAKUSA 8.88 7.72 90 74.86
MAMMOTH 1834.18 1594.94 100 94.01
CE 22053.32 19176.80 98 90.78
  1. aThe top-ranked family in the hit list of a query was used as the predicted family. Accuracy is the percentage of times that the family was correctly predicted.
  2. bThe precision is defined as T/H, where T is the number of true hit structures in the hit list, and H is the total number of structures in the hit list.