Table 2.
Selected features for model construction. The selected features were highly correlated with immunogenicity (indicated by p-value).
| Features | References | Position | Description | p-value |
|---|---|---|---|---|
| ASA | (39) | P3 | Accessible surface area | 0.026 |
| Charged value | (42) | P3 | Net charge | 0.039 |
| ECI | (44) | P3 | Electronic charge index | 0.009 |
| Entropy | (46) | P3 | Entropy of formation | 0.001 |
| Hydrophobicity | (45) | P3 | Modified Kyte-Doolittle hydrophobicity scale, more hydrophobic residues are preferable to be at P4, P7, and P8. | 2.35E-05 |
| ISA | (44) | P3 | Isotropic surface area | 1.62E-06 |
| Mw | (47) | P3 | Molecular weight | 0.042 |
| Organic solvent/water | (50) | P3 | Transfer energy, organic solvent/water | 4.58E-05 |
| Organic solvent/water | (50) | P4 | Transfer energy, organic solvent/water | 0.019 |
| PI | (49) | P5 | Isoelectric point | 0.028 |
| Polarity | (42) | P3 | Polarity | 0.002 |
| Residue propensity | (54) | P1 | Score based on frequency assigned of each amino acid (see Figure 1 ) | 0.000 |
| Residue propensity | (54) | P2 | 0.003 | |
| Residue propensity | (54) | P3 | 2.11E-14 | |
| Residue propensity | (54) | P4 | 4.73E-06 | |
| Residue propensity | (54) | P5 | 4.10E-07 | |
| Residue propensity | (54) | P6 | 8.73E-05 | |
| Residue propensity | (54) | P7 | 2.57E-06 | |
| Residue propensity | (54) | P8 | 1.41E-06 | |
| Residue propensity | (54) | P9 | 0.000 | |
| Residue propensity | (54) | sum | 2.84E-41 | |
| Aff | (7, 52) | binding affinity | 7.64E-08 | |
| Aff_rescale | (52) | Rescale binding affinity | 7.63E-08 | |
| Cle | (7) | C terminal cleavage affinity | 0.003 | |
| Combined score | (7) | Combined prediction score | 3.04E-08 | |
| Pred | (53) | pMHC stability score | 2.42E-08 | |
| Thalf | (53) | pMHC stability score | 0.001 | |
| NB | (53) | pMHC stability score | 1.46E-09 |