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Table 5 Overview of the prediction accuracy of the Small Dataset (242 Residues) II. Three tables show the accuracy of the predictions to the measured pKexp. This is taken as the number of residues predicted within each range. Figures marked in bold indicate significant results (P = 0.05).

From: Benchmarking pKa prediction

TOTAL (242)

          
 

AMBER

 

PARSE

 

MCCE

 

UHBD

 

PROPKA

 
  

%

 

%

 

%

 

%

 

%

<2

195

81

191

79

216

89

225

93

230

95

<1.5

174

72

171

71

201

83

209

86

220

91

<1

131

54

135

56

172

71

161

67

195

81

<0.5

63

26

87

36

110

45

97

40

125

52

SURFACE (209)

          
 

AMBER

 

PARSE

 

MCCE

 

UHBD

 

PROPKA

 
  

%

 

%

 

%

 

%

 

%

<2

179

86

176

84

193

92

199

95

205

98

<1.5

163

78

159

76

181

87

186

89

199

95

<1

126

60

125

60

156

75

152

73

181

87

<0.5

60

29

83

40

100

48

94

45

122

58

BURIED (33)

          
 

AMBER

 

PARSE

 

MCCE

 

UHBD

 

PROPKA

 
  

%

 

%

 

%

 

%

 

%

<2

16

48

15

45

23

70

26

79

25

76

<1.5

11

33

12

36

20

61

23

70

21

64

<1

5

15

10

30

16

48

9

27

14

42

<0.5

3

9

4

12

16

30

3

9

3

9