Table 2 Features used for protein function classification
| Â | Feature | Description | Dimension |
|---|---|---|---|
1 | Number of amino acids | Number of residues in each protein | 1 |
2 | Molecular weight | Molecular weight of the protein | 1 |
3 | Theoretical pI | The pH at which the net charge of the protein is zero (isoelectric point) | 1 |
4 | Amino acid composition | Percentage of each amino acid in the protein | 20 |
5 | Positively charged residue_2 | Percentage of positively charged residues in the protein (lysine and arginine) | 1 |
6 | Positively charged residue_3 | Percentage of positively charged residues in the protein (histidine, lysine, and arginine) | 1 |
7 | Number of atoms | Total number of atoms | 1 |
8 | Carbon | Total number of carbon atoms in the protein sequence | 1 |
9 | Hydrogen | Total number of hydrogen atoms in the protein sequence | 1 |
10 | Nitrogen | Total number of nitrogen atoms in the protein sequence | 1 |
11 | Oxygen | Total number of oxygen atoms in the protein sequence | 1 |
12 | Sulphur | Total number of sulphur atoms in the protein sequence | 1 |
13 | Extinction coefficient_All | Amount of light a protein absorbs at a certain wavelength (assuming ALL Cys residues appear as half cysteines) | 1 |
14 | Extinction coefficient_No | Amount of light a protein absorbs at a certain wavelength (assuming NO Cys residues appear as half cysteines) | 1 |
15 | Instability index | The stability of the protein | 1 |
16 | Aliphatic index | The relative volume of the protein occupied by aliphatic side chains | 1 |
17 | GRAVY | Grand average of hydropathicity | 1 |
18 | PPR | Percentage of continuous changes from positively charged residues to positively charged residues | 1 |
19 | NNR | Percentage of continuous changes from negatively charged residues to negatively charged residues | 1 |
20 | PNPR | Percentage of continuous changes from positively charged residues to negatively charged residues or from negatively charged residues to positively charged residues | 1 |
21 | NNRDist (x, y) | Percentage of NNR from x to y (local information) | 10 |
22 | PPRDist (x, y) | Percentage of PPR from x to y (local information) | 10 |
23 | PNPRDist (x, y) | Percentage of PNPR from x to y (local information) | 10 |
24 | Charged | Physicochemical property | 1 |
25 | Negatively charged residues | Percentage of negatively charged residues in the protein | 1 |
26 | Polar | Physicochemical property | 1 |
27 | Aliphatic | Physicochemical property | 1 |
28 | Aromatic | Physicochemical property | 1 |
29 | Small | Physicochemical property | 1 |
30 | Tiny | Physicochemical property | 1 |
31 | Bulky | Physicochemical property | 1 |
32 | Hydrophobic | Physicochemical property | 1 |
33 | Hydrophobic and aromatic | Physicochemical properties | 1 |
34 | Neutral, weakly and hydrophobic | Physicochemical properties | 1 |
35 | Hydrophilic and acidic | Physicochemical properties | 1 |
36 | Hydrophilic and basic | Physicochemical properties | 1 |
37 | Acidic | Physicochemical property | 1 |
38 | Polar and uncharged | Physicochemical properties | 1 |
39 | Amino acid pair ratio | Percentage compositions for each of the 400 possible amino acid dipeptides | 400 |
| Â | Total | Â | 484 |