TABLE 2.
Docking performance of individual targets
| Ligand PDB | Domain level |
Complex level (I-RMSD, Å) |
|||||||
|---|---|---|---|---|---|---|---|---|---|
| CAPRI-acceptable hits | Best fnat in top 10 | Best I-RMSD in top 10 (Å) | Best L-RMSD in top 10 (Å) | Flex-fitting-to-native | Rigid-body LZerD | Top-scored | Best in top 10 | Best in all | |
|
| |||||||||
| 3NDB | 8/1 | 0.22/0.10 | 1.58/4.90 | 3.40/10.95 | 4.05 | (14.84) | 6.88 | 6.68 | 5.75 |
| 2RDI | 7/5 | 0.30/0.42 | 2.45/1.33 | 5.17/3.01 | 3.86 | (14.10) | 4.97 | 4.97 | 4.10 |
| *3FDS | 1/1 | 0.59/0.43 | 1.99/4.92 | 4.39/5.68 | 5.54 | (15.33) | 11.04 | 11.04 | 9.58 |
| *1BPD | 5/6 | 0.50/0.29 | 2.69/2.94 | 7.46/5.18 | 2.04 | (11.58) | 4.54 | 4.48 | 4.48 |
| 1ZBH | 13/2 | 0.34/0.27 | 0.91/2.62 | 3.03/9.23 | 1.58 | (11.25) | 4.63 | 4.63 | 3.01 |
| 5F6C | 12/0 | 0.25/0.29 | 2.07/6.66 | 11.40/30.46 | 1.97 | 2.32 | 3.98 | 3.98 | 3.51 |
| 5KDM | 0/0 | 0.07/0.04 | 0.62/8.51 | 3.6/23.33 | 1.45 | (12.77) | (11.42) | (11.41) | (8.77) |
| 1NFI | 2/9 | 0.24/0.43 | 2.24/0.89 | 6.95/2.51 | 4.34 | (7.83) | 4.57 | 4.57 | 4.11 |
| *5WH1 | 8/3 | 0.16/0.11 | 2.20/0.12 | 5.55/1.98 | 2.45 | (8.73) | 4.08 | 4.08 | 4.08 |
| 2AS5 | 11/9 | 0.35/0.23 | 1.49/1.42 | 6.66/4.39 | 2.78 | (10.45) | 4.61 | 4.61 | 2.85 |
| *1GV2 | 2/3 | 0.81/0.76 | 1.92/0.92 | 4.14/1.90 | 2.08 | (6.13) | 3.39 | 3.31 | 3.03 |
| 4ZV4 | 0/16 | 0.10/0.51 | 4.96/1.60 | 12.16/4.02 | 3.59 | (10.87) | (10.21) | (10.21) | (9.47) |
| *1AIP | 1/4 | 0.89/0.77 | 3.74/1.86 | 15.98/4.52 | 2.75 | (8.30) | 4.09 | 4.09 | 4.08 |
| 6APC | 1/6 | 0.25/0.16 | 2.88/3.24 | 6.99/6.15 | 1.91 | (5.99) | (15.24) | (14.77) | 3.82 |
| *1FGU | 7/3 | 0.70/0.45 | 1.71/3.86 | 3.74/7.57 | 1.62 | (9.56) | 5.91 | 5.43 | 5.40 |
| *4ON9 | 6/2 | 0.69/0.17 | 2.15/5.78 | 5.18/8.98 | 2.51 | (11.22) | 4.69 | 4.68 | 4.59 |
| *5MGU | 0/0 | 0.41/0.11 | 4.99/6.45 | 19.77/16.99 | 4.99 | (14.22) | 8.26 | 6.92 | 6.92 |
Targets are identified by their ligand PDB IDs. “/” indicates that the two numbers given are for the first and second domains, respectively. Domain hits, the number of CAPRI-acceptable quality domains within the top 100 by the combined scoring function. Numbers given in parentheses indicate models which did not meet the CAPRI-acceptable quality criteria. Flexible-fitting-to-native results are for the single output model generated when performing flexible fitting of the unbound structure directly to the bound native structure. Rigid-body LZerD results showthe best I-RMSD in the entire rigid-body LZerD pipeline output set using the unbound ligand conformation, typically tens of thousands of models. Asterisks (*) indicate targets also present in the original Flex-LZerD dataset. I-RMSD, interface RMSD; L-RMSD, ligand RMSD; PDB, Protein Data Bank; RMSD, root-mean-square deviation.