Table 2 Performance of six pairwise structure alignment tools on benchmarks MALIDUP and MALISAM

MALIDUP

DeepAlign ^∗

85.5

2.61

0.622

10.2

DALI ^∗

83.5

2.65

0.600

115.3

MATT ^∗

82.3

2.47

0.608

63.0

Formatt ^∗

70.6

2.19

0.542

85.1

TM-align ^∗

87.0

2.62

0.631

6.4

MADOKA

91.7

3.43

0.631

1.2

MALISAM

DeepAlign ^∗

61.3

2.96

0.521

4.3

DALI ^∗

61.0

3.11

0.515

47.4

MATT ^∗

56.2

2.74

0.486

16.2

Formatt ^∗

44.9

2.42

0.411

33.1

TM-align ^∗

61.1

3.06

0.517

2.9

MADOKA

62.8

2.72

0.555

0.7