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Table 1 Full list of the 80 biochemical properties used in the FEATURE program

From: 3D deep convolutional neural networks for amino acid environment similarity analysis

1

ATOM_TYPE_IS_C

41

RESIDUE_NAME_IS_GLU

2

ATOM_TYPE_IS_CT

42

RESIDUE_NAME_IS_GLY

3

ATOM_TYPE_IS_CA

43

RESIDUE_NAME_IS_HIS

4

ATOM_TYPE_IS_N

44

RESIDUE_NAME_IS_ILE

5

ATOM_TYPE_IS_N2

45

RESIDUE_NAME_IS_LEU

6

ATOM_TYPE_IS_N3

46

RESIDUE_NAME_IS_LYS

7

ATOM_TYPE_IS_NA

47

RESIDUE_NAME_IS_MET

8

ATOM_TYPE_IS_O

48

RESIDUE_NAME_IS_PHE

9

ATOM_TYPE_IS_O2

49

RESIDUE_NAME_IS_PRO

10

ATOM_TYPE_IS_OH

50

RESIDUE_NAME_IS_SER

11

ATOM_TYPE_IS_S

51

RESIDUE_NAME_IS_THR

12

ATOM_TYPE_IS_SH

52

RESIDUE_NAME_IS_TRP

13

ATOM_TYPE_IS_OTHER

53

RESIDUE_NAME_IS_TYR

14

PARTIAL_CHARGE

54

RESIDUE_NAME_IS_VAL

15

ELEMENT_IS_ANY

55

RESIDUE_NAME_IS_HOH

16

ELEMENT_IS_C

56

RESIDUE_NAME_IS_OTHER

17

ELEMENT_IS_N

57

RESIDUE_CLASS1_IS_HYDROPHOBIC

18

ELEMENT_IS_O

58

RESIDUE_CLASS1_IS_CHARGED

19

ELEMENT_IS_S

59

RESIDUE_CLASS1_IS_POLAR

20

ELEMENT_IS_OTHER

60

RESIDUE_CLASS1_IS_UNKNOWN

21

HYDROXYL

61

RESIDUE_CLASS2_IS_NONPOLAR

22

AMIDE

62

RESIDUE_CLASS2_IS_POLAR

23

AMINE

63

RESIDUE_CLASS2_IS_BASIC

24

CARBONYL

64

RESIDUE_CLASS2_IS_ACIDIC

25

RING_SYSTEM

65

RESIDUE_CLASS2_IS_UNKNOWN

26

PEPTIDE

66

SECONDARY_STRUCTURE1_IS_3HELIX

27

VDW_VOLUME

67

SECONDARY_STRUCTURE1_IS_4HELIX

28

CHARGE

68

SECONDARY_STRUCTURE1_IS_5HELIX

29

NEG_CHARGE

69

SECONDARY_STRUCTURE1_IS_BRIDGE

30

POS_CHARGE

70

SECONDARY_STRUCTURE1_IS_STRAND

31

CHARGE_WITH_HIS

71

SECONDARY_STRUCTURE1_IS_TURN

32

HYDROPHOBICITY

72

SECONDARY_STRUCTURE1_IS_BEND

33

MOBILITY

73

SECONDARY_STRUCTURE1_IS_COIL

34

SOLVENT_ACCESSIBILITY

74

SECONDARY_STRUCTURE1_IS_HET

35

RESIDUE_NAME_IS_ALA

75

SECONDARY_STRUCTURE1_IS_UNKNOWN

36

RESIDUE_NAME_IS_ARG

76

SECONDARY_STRUCTURE2_IS_HELIX

37

RESIDUE_NAME_IS_ASN

77

SECONDARY_STRUCTURE2_IS_BETA

38

RESIDUE_NAME_IS_ASP

78

SECONDARY_STRUCTURE2_IS_COIL

39

RESIDUE_NAME_IS_CYS

79

SECONDARY_STRUCTURE2_IS_HET

40

RESIDUE_NAME_IS_GLN

80

SECONDARY_STRUCTURE2_IS_UNKNOWN

  1. Description of each property can be found in [63]
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BMC Bioinformatics

ISSN: 1471-2105

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