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Table 2 Average search time and mean average precision of each program on 108 queries in SCOP-108

From: Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database

Program Mean of average precision Total searching time (s) Average time per query (s) Related to 3D-BLAST
PSI-BLASTa 69.8% 18.31 0.170 0.533
3D-BLAST 78.2% 34.35 0.318 1
MAMMOTHb 82.1% 131,855 1220.88 3838.58
CE 83.4% ~13.5 days ~3 hours ~34000
  1. Time was measured using a personal computer equipped with an Intel Pentium 2.8 GHz processor with 1,024 megabytes of RAM memory. aPSI-BLAST used E values to rank the hit proteins. bMAMMOTH and CE utilized Z scores to rank hit proteins.