Table II.
The Performance of DockRank on Cases That Have More Than Two Chains But Only a Subset of Chains Have Templates
| Case ID (level of conformational changes) | ClusPro2-BM3 |
ZDock3-BM3 |
PS-HomPPI Interface predictiona | ||||
|---|---|---|---|---|---|---|---|
| DockRank | ClusPro | DockRank | IRAD | ZRank | |||
| Group 1 | 1GP2 (medium) | – | – | Acceptable (1) | Acceptable (85) | Acceptable (133) | Very Good for two chains |
| 1K5D (medium) | – | – | Medium (2) Acceptable (1) | Medium (933) Acceptable (12) | Medium (4295) Acceptable (84) | Very Good for two chains | |
| 1JM0 (difficult) | – | – | Acceptable (3168) | NO RANKING | Acceptable (44899) | Very Good for two chains | |
| 1F51 (rigid-body) | Acceptable (1) | Acceptable (15) | High (2) Medium (1) Acceptable (6) | High (10918) Medium (1) Acceptable (13) | High (15370) Medium (3) Acceptable (67) | Good for one chain, ok for another chain. | |
| Group II | 1E6J (rigid-body) | Acceptable (18) | Acceptable (9) | Medium (22169) Acceptable (7037) | Medium (2) Acceptable (17) | Medium (1) Acceptable (8) | Good for one chain. |
| 2FD6 (rigid-body) | – | – | Medium (25373) Acceptable (9277) | Medium (21) Acceptable (1) | Medium (63) Acceptable (15) | Ok for one chain. | |
| Group III | 2HMI (difficult) | – | – | Acceptable (23048) | NO RANKING | Acceptable (272) | Bad |
According to the CARPI criteria, a docked model is classified into four categories: (1) a high-quality model, if its I–RMSD ≤ 1Å; (2) a medium quality model, if its I–RMSD ≤ 2Å; (3) an acceptable model if its I–RMSD ≤ 4Å.
The numbers in the parentheses are the ranks of the first model belonging to the corresponding category.
a
See Supporting Information Table S5 for details.