Table 3.

Average search time of each program on 108 queries in the SCOP 1.59. Results for all the methods except ours are taken from [33]. Their experiments were performed on a computer with an Intel Pentium 2.8 GHz processor and 1,024 megabytes of RAM memory. Ours were done on a computer with Intel Pentium 2.66 GHz processor and 1,024 megabytes of RAM memory.

Software	Total search time (s)	Average search time per query (s)
Our method	12,117	112.20
3D-Blast	34.35	0.318
PSI-BLAST	18.31	0.170
CE	13.5 days	3 hours
MAMMOTH	131,855	1220.88