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Table 2 Speed comparisons for 108 queries on a database of 34055 proteins

From: Protein structural similarity search by Ramachandran codes

Method

Average time per query (sec)

Average time per comparison (sec)

Relative to SARST

CE

82789.20

2.43E+00

243497.65

FAST

6241.57

1.83E-01

18357.56

TOPSCANa

85.08

2.50E-03

250.24

YAKUSA

35.6

1.05E-03

104.71

3D-BLAST

9.07

2.66E-04

26.68

ProtDex2

0.76

2.23E-05

2.24

BLAST

0.30

8.76E-06

0.88

SARST

0.34

9.98E-06

1.00

SARST (2 CPUsb)

0.16

4.70E-06

0.47

  1. aThese results were adapted from Aung and Tan's report [30].
  2. bTwo hyperthreading 3.2 GHz CPUs were used to obtain these results, others were calculated using one CPU.