Table 3.
Cross‐docking with flexible side chains for SEQ17 dataset
| Holo | Apo | Num. of Rot. bonds | Rank of lowest RMSD pose with RMSD < 2.5 Å | Runtime (min) | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Lig | Rec | Tot | vina | autodockfr | gwo vina | vina | autodockfr | gwo vina | ||
| 1IT8 | 1IQ8 | 1 | 11 | 12 | 1 | 1 | 1 | 0.47 | 11.14 | 0.13 |
| 1K4H | 1PUD | 5 | 19 | 24 | 1 | 1 | 1 | 2.29 | 35.62 | 0.47 |
| 1GX9 | 1BSQ | 5 | 27 | 32 | 10 (–) | 1 | 1 | 4.86 | 38.38 | 0.90 |
| 2H8H | 1FMK | 4 | 16 | 20 | – | 4 (1) | 12 | 3.01 | 35.09 | 0.79 |
| 3JRX | 2HJW | 6 | 30 | 36 | 1 | –(1) | 1 | 12.93 | 49.42 | 1.74 |
| 1Z6P | 2GPN | 7 | 24 | 31 | – | –(2) | 5 | 6.95 | 41.96 | 1.31 |
| 1AQ1 | 1HCL | 2 | 22 | 24 | – | 7 (2) | – | 4.01 | 36.85 | 0.59 |
| 1QKJ | 2BGT | 8 | 24 | 32 | – | –(3) | 4 | 4.63 | 34.45 | 0.79 |
| 1LNM | 1KXO | 3 | 27 | 30 | 3 (4) | 3 | 2 | 14.82 | 51.54 | 1.74 |
| 1IKG | 3PTE | 13 | 28 | 41 | 1 | – (14) | 1 | 17.75 | Fail to run | 2.29 |
| 1C1H | 1DOZ | 8 | 31 | 39 | – | – (14) | 12 | 19.91 | 43.39 | 2.72 |
| 3ERK | 1ERK | 4 | 20 | 24 | – | 4 (14) | 21 | 2.48 | 40.30 | 0.47 |
| 1RBP | 1BRQ | 6 | 18 | 24 | – (6) | – | 3 | 1.75 | 17.82 | 0.36 |
| 1BR5 | 1RTC | 7 | 16 | 23 | – | – | – | 2.48 | 37.30 | 0.36 |
| 1YXT | 1XQZ | 6 | 27 | 33 | – | – | – | 7.65 | 49.28 | 1.64 |
| 1ZG3 | 1ZHF | 4 | 18 | 22 | – | – | – | 2.04 | 39.72 | 0.42 |
| 2A9K | 2A78 | 16 | 36 | 52 | – | – | – | 31.98 | 94.62 | 4.22 |
| Total | 6 (6) | 7 (12) | 12 | 140.12 | 656.88 | 20.94 | ||||
| Percentage | 35% (35%) | 41% (71%) | 71% | |||||||
The docking that did not produce any poses with RMSD <= 2.5 Å is indicated by the symbol “–“.
The docking result reported in (Ravindranath et al., 2015) that is different from our own experimental result is given in brackets.