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

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

Program	Mean of average precision	Total searching time (s)	Average time per query (s)	Related to 3D-BLAST
PSI-BLAST^a	69.8%	18.31	0.170	0.533
3D-BLAST	78.2%	34.35	0.318	1
MAMMOTH^b	82.1%	131,855	1220.88	3838.58
CE	83.4%	~13.5 days	~3 hours	~34000

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.

ISSN: 1474-760X