Table 1 Protein descriptors commonly used for predicting protein functional families.
From: Efficacy of different protein descriptors in predicting protein functional families
Sets | Descriptor-sets | No. of descriptors (properties) | No. of components | Type | Physicochemical properties | Refs |
|---|---|---|---|---|---|---|
D1 | Amino acid composition | 1 | 20 | Sequence composition | Â | [23] |
D2 | Dipeptide composition | 1 | 400 | Sequence composition | Â | [24] |
D3 | Normalized Moreau – Broto autocorrelation | 8 | 240 | Correlation of physicochemical properties | Hydrophobicity scale, average flexibility index, polarizability parameter, free energy of amino acid solution in water, residue accessible surface area, amino acid residue volume, steric parameters, relative mutability | [25, 26] |
D4 | Moran autocorrelation | 8 | 240 | Correlation of physicochemical properties | Hydrophobicity scale, average flexibility index, polarizability parameter, free energy of amino acid solution in water, residue accessible surface area, amino acid residue volume, steric parameters, relative mutability | [27] |
D5 | Geary autocorrelation | 8 | 240 | Square correlation of physicochemical properties | Hydrophobicity scale, average flexibility index, polarizability parameter, free energy of amino acid solution in water, residue accessible surface area, amino acid residue volume, steric parameters, relative mutability | [28] |
D6 | Descriptors of composition, transition and distribution | 21 | 147 | Distribution and variation of physicochemical properties | Hydrophobicity, Van der Waals volume, polarity, polarizability, charge, secondary structures, solvent accessibility | [2-6, 8, 17, 29, 30] |
D7 | Quasi sequence order | 4 | 160 | Combination of sequence composition and correlation of physicochemical | Hydrophobicity, hydrophilicity, polarity, side-chain volume | [10, 11, 18, 31] |
D8 | Pseudo amino acid composition | 3 | 298 | Combination of sequence composition and square correlation of physicochemical | Hydrophobicity, hydrophilicity, side chain mass | [23, 32] |
D9 | Combination of amino acid and dipeptide composition | 2 | 420 | Combination of sequence compositions | Â | Â |
D10 | Combination of all eight sets of descriptors | 54 | 1745 | Combination of all sets | Â | Â |