Skip to main content

Table 2 Improvement of the performance of the AutoMotifServer 3.0.

From: AMS 3.0: prediction of post-translational modifications

  

AMS 2.0

AMS 3.0

AMS 3.0 (New SwissProt dataset)

PTM type

Agent

Recall

Precision

Recall

Precision

AUC

Recall

Precision

AUC

3,4-dihydroxyproline

-

88,89

66,67

95,45

87,5

0,962273

97,37

97,37

0,985088

4-carboxyglutamate

-

90,56

95,93

96,27

99,65

0,980856

96,54

99,35

0,982076

4-hydroxyproline

-

65,59

85,31

86,88

83,94

0,905902

95,03

94,14

0,969559

5-hydroxylysine

-

12,79

84,62

97,3

38,92

0,845236

90,16

95,93

0,948272

Asymmetric dimethylarginine

-

84,62

82,09

94,55

94,55

0,965227

-

-

-

dihydroxyphenylalanine

-

29,41

76,92

86,17

86,17

0,914601

-

-

-

Glycine amide

-

84,38

90

97,92

97,92

0,977679

99,3

99,3

0,984574

Hydroxyproline

-

28,8

85,71

89,62

94,06

0,942113

94,62

99,19

0,972567

Leucine amide

-

98,97

97,96

98,1

99,36

0,989049

-

-

-

Methionine amide

-

100

93,75

100

93,75

0,666667

-

-

-

N-acetylglycine

-

79,17

90,48

97,83

97,83

0,985797

-

-

-

N-acetylmethionine

-

100

95,42

98,4

98,93

0,990593

-

-

-

N-acetylserine

-

98,24

99,64

98,22

99,4

0,990124

-

-

-

N-acetylthreonine

-

76,47

88,64

89,8

97,78

0,94648

-

-

-

N6-acetyllysine

-

12,76

74,32

94,3

93,23

0,953465

-

-

-

N6, N6, N6-trimethyllysine

-

7,5

60

85,71

97,5

0,926065

-

-

-

Omega-N-methylated arginine

-

0

0

78

58,21

0,82

-

-

-

Phenylalanine amide

-

98,59

93,33

99

99

0,986667

-

-

-

Phospho

PKA

63,64

77,78

90,72

86,27

0,939608

97,39

95,39

0,983802

Phospho

PKC

32,56

84,85

86,17

97,59

0,928851

94,78

99,18

0,973369

Phospho

autocatalysis

13,16

96,15

79,35

93,59

0,888392

95,96

99,15

0,97851

Phospho

CDC2

85,71

80,9

89,55

75,95

0,916095

93,73

92,36

0,963488

Phosphoserine

-

97,06

91,34

94,33

95,56

0,94975

96,87

98,02

0,912848

Phosphoserine

PKA

68,42

78,31

91,67

72,64

0,922083

97,66

98,43

0,987096

Phosphoserine

PKC

23,29

80,95

96,43

95,29

0,975476

94,93

98,94

0,973939

Phosphoserine

autocatalysis

10

85,71

75

90,7

0,868311

91,57

99,13

0,957295

Phosphoserine

CK2

29,73

70,97

88,14

59,77

0,882345

93,02

98,23

0,962999

Phosphothreonine

-

46,12

75,46

78,16

69,73

0,828495

85,2

97,4

0,905598

Phosphothreonine

autocatalysis

0

0

73,47

80

0,849347

94,96

99,82

0,974381

Phosphotyrosine

-

9,32

71,2

84,24

96,69

0,91775

91,75

98,97

0,952053

Phosphotyrosine

autocatalysis

1,41

12,5

92

92

0,951404

96,82

97,21

0,979045

Pyrrolidone carboxylic acid

-

60,31

97,11

91,58

97,92

0,955236

-

-

-

Sulfotyrosine

-

70,19

85,88

98,39

97,6

0,988929

99,48

98,47

0,990853

Valine amide

-

94,29

97,06

98,57

98,57

0,986607

-

-

-

Phospho.ELM

-

98

91,68

-

-

-

98,56

96,07

0,949397

Phospho.ELM

Abl

0

0

-

-

-

81,82

52,94

0,862032

Phospho.ELM

AMPK_group

6,25

100

-

-

-

100

72,22

0,975

Phospho.ELM

ATM

92,98

81,54

-

-

-

94,87

90,24

0,967439

Phospho.ELM

CaM-KIIalpha

41,67

88,24

-

-

-

100

77,42

0,981081

Phospho.ELM

CaM-KII_group

14,55

88,89

-

-

-

82,05

94,12

0,906796

Phospho.ELM

CDK1

41,73

63,04

-

-

-

96,94

62,91

0,94711

Phospho.ELM

CDK2

7,14

45,45

-

-

-

92,31

64,86

0,928627

Phospho.ELM

CDK_group

59,8

67,03

-

-

-

95,65

67,35

0,947785

Phospho.ELM

CK1_group

0

0

-

-

-

86,67

72,22

0,911594

Phospho.ELM

CK2 alpha

38,98

67,65

-

-

-

78,82

70,53

0,872036

Phospho.ELM

CK2_group

43,33

72,22

-

-

-

73,33

64,36

0,839759

Phospho.ELM

EGFR

0

0

-

-

-

73,17

78,95

0,852909

Phospho.ELM

Fyn

0

0

-

-

-

87,5

84,85

0,9275

Phospho.ELM

GRK_group

2,7

100

-

-

-

83,33

90,91

0,911404

Phospho.ELM

GSK-3beta

18,37

75

-

-

-

85,29

64,44

0,896282

Phospho.ELM

GSK-3_group

12,5

66,67

-

-

-

65,22

93,75

0,823128

Phospho.ELM

IGF1R

26,09

100

-

-

-

85

73,91

0,90625

Phospho.ELM

IKK_group

0

0

-

-

-

95,83

92

0,973761

Phospho.ELM

InsR

6,67

60

-

-

-

70,97

88

0,848289

Phospho.ELM

Lck

11,76

60

-

-

-

80,56

74,36

0,884596

Phospho.ELM

Lyn

0

0

-

-

-

66,67

84,62

0,825137

Phospho.ELM

MAPK1

45,88

67,24

-

-

-

88,98

55,85

0,898547

Phospho.ELM

MAPK14

4

22,22

-

-

-

82,35

77,78

0,896017

Phospho.ELM

MAPK3

74,7

78,48

-

-

-

87,93

77,27

0,922801

Phospho.ELM

MAPK8

14,71

41,67

-

-

-

91,67

84,62

0,947523

Phospho.ELM

MAPKAPK2

3,03

100

-

-

-

69,57

80

0,836332

Phospho.ELM

MAPK_group

54,9

77,78

-

-

-

82,35

75,68

0,894784

Phospho.ELM

PDK-1

42,86

85,71

-

-

-

80

95,24

0,897283

Phospho.ELM

PKA alpha

42,42

82,35

-

-

-

86,96

95,24

0,931824

Phospho.ELM

PKA_group

58,15

90,43

-

-

-

91,74

62,99

0,904783

Phospho.ELM

PKB_group

79,76

65,05

-

-

-

88,14

77,61

0,924011

Phospho.ELM

PKC alpha

19,7

72,22

-

-

-

75,56

48,57

0,825223

Phospho.ELM

PKC_group

25,21

80

-

-

-

82,02

84,39

0,900038

Phospho.ELM

PLK1

0

0

-

-

-

68,97

45,45

0,788753

Phospho.ELM

Src

0,67

5

-

-

-

74,31

65,32

0,845308

Phospho.ELM

Syk

6,67

30

-

-

-

85,71

53,57

0,878378

  1. Comparison of best performances of the AMS 2.0 server with the current AMS version 3.0 on best results obtained on the training datasets of respective PTM types.
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us