Table 4.
Prediction performances on five types of SARS-Cov-2 BCEs and best values are in bold.
| Epitopes (PDB ID and chains name) | Methods | Precision | Recal | MCC |
|---|---|---|---|---|
| Type 1 (7K8M_AB_E) | Discotope-2.0 | 0.660 | 0.649 | 0.297 |
| Epipred | 0.402 | 0.401 | -0.199 | |
| PECAN | 0.638 | 0.583 | 0.143 | |
| Our method | 0.576 | 0.631 | 0.200 | |
| Type 2 (6YOR_HL_E) | Discotope-2.0 | 0.432 | 0.430 | -0.140 |
| Epipred | 0.431 | 0.423 | -0.153 | |
| PECAN | 0.494 | 0.492 | -0.016 | |
| Our method | 0.664 | 0.658 | 0.322 | |
| Type 3 (7K43_HL_A) | Discotope-2.0 | 0.526 | 0.554 | 0.095 |
| Epipred | 0.493 | 0.489 | -0.021 | |
| PECAN | 0.531 | 0.545 | 0.086 | |
| Our method | 0.525 | 0.773 | 0.166 | |
| Type 4 (7BWJ_HL_E) | Discotope-2.0 | 0.589 | 0.615 | 0.226 |
| Epipred | 0.494 | 0.491 | -0.017 | |
| PECAN | 0.555 | 0.591 | 0.171 | |
| Our method | 0.684 | 0.847 | 0.506 | |
| Type 5 (7CWU_PI_C) | Discotope-2.0 | 0.547 | 0.641 | 0.226 |
| Epipred | 0.494 | 0.490 | -0.019 | |
| PECAN | 0.579 | 0.626 | 0.240 | |
| Our method | 0.494 | 0.500 | 0.000 |
The PDB ID and chains name of representative complex structures are shown as PDB ID_Antibody heavy chain and light chain name_ Antigen (SARS-Cov-2) chain name. The results of Discotope-2.0 and Epipred are obtained from their websites using suggested threshold. For PECAN, we download its source code and run it for making comparison. It should be noted that Epipred and PECAN take both antigen and its partner antibody structure as input. Discotope-2.0 and our method only utilize isolated antigen structure.