Table 1 Comparisons of structure alignment algorithms with rms distance and the number of aligned atoms m.

rms

m

λ

rms

m

rms

m

rms

m

Reductases

1DHF _a - 8DFR

0.7

182

6.0

0.7

182

0.7

182

0.7

182

1DHF _a - 4DFR _a

1.8

156

6.0

2.0

154

2.0

154

2.0

156

1DHF _a - 3DFR

1.6

159

6.0

1.7

158

1.7

158

1.7

159

8DFR - 4DFR _a

1.9

157

6.0

2.0

155

2.0

155

2.0

157

8DFR - 3DFR

1.6

159

6.0

1.8

159

1.8

158

1.8

160

4DFR _a - 3DFR

1.5

156

6.0

1.5

154

1.5

155

1.5

155

Globins

2HHB _a - 2HHB _b

1.4

139

6.0

1.4

138

1.5

139

1.4

139

2HHB _a - 1MBD

1.5

141

6.0

1.5

139

1.6

141

1.5

141

2HHB _a - 2HBG

1.6

140

6.0

1.7

138

1.7

136

1.6

138

2HHB _a - 1ECD

2.2

131

6.0

2.3

129

2.6

128

2.3

130

1MBD - 2HBG

2.0

141

8.0

2.2

140

2.1

140

2.0

140

2HHB _b - 1MBD

1.6

145

6.0

1.6

145

1.6

144

1.6

145

2HHB _b - 2HBG

1.7

137

6.0

2.0

135

1.9

134

1.7

136

2HHB _b - 1MBA

2.2

140

6.0

2.3

138

2.4

139

2.4

140

2LHB - 1MBD

1.4

137

6.0

1.4

135

1.6

137

1.5

137

2LHB - 2HBG

1.9

133

6.0

2.0

128

2.1

130

2.0

132

1MBD - 1MBA

1.9

143

6.0

1.9

142

1.8

141

1.9

143

1MBA - 1ECD

1.9

136

8.0

1.9

133

2.0

134

2.0

136

2HBG - 1ECD

2.4

129

6.5

2.6

129

2.6

125

2.5

129

Ten 'difficult' structures

1FXI _a - 1UBQ

2.5

70

6.0

2.6

60

3.8

64

2.6

63

1TEN - 3HHR _b

1.7

87

6.0

1.9

86

1.9

87

1.8

87

3HLA _b - 2RHE

2.9

87

6.0

3.0

75

3.4

84

3.3

83

2AZA _a - 1PAZ

2.5

82

4.5

2.5

81

2.9

84

2.4

83

1CEW _i - lMOL _a

2.3

83

6.5

2.3

81

2.3

81

2.2

82

1CID - 2RHE

2.3

98

6.5

3.2

97

2.9

97

2.5

97

1CRL - 1EDE

3.1

281

6.0

3.5

211

3.8

219

5.0

126

2SIM - 1NSB _a

2.9

322

6.0

3.3

291

3.0

275

2.9

292

1BGE _b - 2GMF _a

3.3

110

7.5

3.3

94

3.9

107

3.3

104

1TIE - 4FGF

2.4

115

6.0

3.1

114

2.9

116

2.7

115

Different folds

1NSB _a - 1TIE

3.1

156

6.0

-

6.4

88

-

1NSB _a - 4FGF

3.0

118

6.0

-

5.8

72

-

1FXI _a - 1CEW _i

2.9

56

6.0

-

7.2

56

-

1FXI _a - 1MOL _a

2.9

70

6.0

-

5.8

48

-

Different Classes

1BGE _b - 1TEN

2.8

82

6.0

-

7.4

40

-

1BGE _b - 1PAZ

3.2

103

6.0

-

6.2

48

-

2GMF _a - 1TEN

3.0

68

6.0

-

4.8

40

-

Circular permutation

1LED - 1NLS

1.1

213

6.0

1.9

119

1.1

112

-

2PIA - 1AXJ

3.3

118

6.0

3.49

36

3.3

62

-