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Table 7 Average running time of the methods to search in a database of 34,055 proteins (in seconds)

From: TS-AMIR: a topology string alignment method for intensive rapid protein structure comparison

Method

Average time per query

Average time per comparison

CE

82789.20

2.43

TM-align

9273.41

0.272

YAKUSA

35.60

0.00105

TS-AMIR

11.47

0.000337

3D-BLAST

9.07

0.000266

SARST

0.34

0.00000998

  1. - Except for TM-align and TS-AMIR, the Results were taken from literature [22].
  2. - The experiments were done on a 3.2 GHz CPU.
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Algorithms for Molecular Biology

ISSN: 1748-7188