Table 1.
Antibody–antigen complexes used for cross-docking.
| No. | Antibody | Antigen | Complex PDB | Antibody PDB | Antigen PDB | Expt. Kd (nM) |
|---|---|---|---|---|---|---|
| 1 | Fab B02C11 | Factor VIII domain C2 | 1IQD | 1IQD* | 1D7P | <0.014 |
| 2 | Fab N10 | Staphylococcal nuclease | 1NSN | 1NSN* | 1KDC | <0.10 |
| 3 | Fab D3H44 | Tissue factor | 1JPS | 1JPT | 1TFH | 0.10 |
| 4 | FabF10.6.6 | HEW lysozyme | 1P2C | 2Q76 | 3LZT | 0.10 |
| 5 | Fab BV16 | Birch pollen antigen Bet V1 | 1FSK | 1FSK* | 1BV1 | 0.24 |
| 6 | Fab E8 | Cytochrome C | 1WEJ | 1QBL | 1HRC | 0.71 |
| 7 | Fab HC19 | Flu virus hemagglutinin | 2VIR | 1GIG | 2HMG | 1.00 |
| 8 | Fab Hyhel63 | HEW lysozyme | 1DQJ | 1DQQ | 3LZT | 2.80 |
| 9 | Fab Jel42 | HPr | 2JEL | 2JEL* | 1POH | 2.80 |
| 10 | Fab 5g9 | Tissue factor | 1AHW | 1FGN | 1TFH | 3.40 |
| 11 | Fab A4.6.1 | VEGF | 1BJ1 | 1BJ1* | 2VPF | 3.40 |
| 12 | Fv D1.3 | HEW lysozyme | 1VFB | 1VFA | 8LYZ | 3.70 |
| 13 | Fab NC41 | Flu virus neuraminidase N9 | 1NCA | 1NCA* | 7NN9 | 8.30 |
| 14 | Fv Hulys11 | HEW lysozyme | 1BVK | 1BVL | 3LZT | 14 |
| 15 | Fab 13B5 | HIV-1 capsid protein p24 | 1E6J | 1E6O | 1A43 | 29 |
| 16 | Fab 44.1 | HEW lysozyme | 1MLC | 1MLB | 3LZT | 91 |
| 17 | Fab HC19 | Flu virus hemagglutinin T131I mutant | 2VIS | 1GIG | 2VIU | 4000 |
*In these six cases, the only antibody structure available is in the antigen-bound state.