Table 2.
Results of the pocket analysis as performed by Pockets 2.0 on the therapeutically relevant protein targets. The first part of the Table includes data concerning the overall search (such as the source of the analyzed protein, the probe ligand and the number of found pockets), while the second part comprises data concerning the search for the correct pocket. In detail, the Table reports how the correct pocket was ranked by FPocket and PLANTS alone and by consensus score, which combines both searches. The volume and the ChemPLP score for the correct pocket are also listed.
| Protein | Protein Data | Data for the Search of the Correct Pocket | ||||||
|---|---|---|---|---|---|---|---|---|
| Source/ID | Ligand | N Pockets | Rank by Fpocket | Rank by PLANTS | Rank by Consensus | Volume (Å3) | ChemPLP (kcal/mol) | |
| 3CL-PRO | 5R7Y | 3WL | 16 | 1 | 1 | 1 | 3604.93 | −76.15 |
| 5R7z | 3WL | 16 | 1 | 1 | 1 | 4246.06 | −73.85 | |
| 5R80 | 3WL | 20 | 2 | 2 | 1 | 1833.23 | −76.48 | |
| 5R81 | 3WL | 17 | 1 | 1 | 1 | 3141.06 | −80.27 | |
| 5R82 | 3WL | 19 | 1 | 4 | 1 | 3989.84 | −68.23 | |
| 5R83 | 3WL | 21 | 1 | 1 | 1 | 4079.17 | −77.59 | |
| 5R84 | 3WL | 21 | 1 | 1 | 1 | 2562.02 | −80.88 | |
| 6LU7 | 3WL | 14 | 1 | 1 | 1 | 4239.62 | −77.83 | |
| 6MN2 dimer | 3WL | 80 | 1 | 1 | 1 | 3344.72 | −86.30 | |
| 6M03 | 3WL | 24 | 3 | 3 | 3 | 2175.81 | −69.70 | |
| 6Y2E | 3WL | 18 | 1 | 4 | 1 | 2629.29 | −75.02 | |
| 6Y2F | 3WL | 20 | 1 | 1 | 1 | 2581.33 | −77.61 | |
| 6Y2G | 3WL | 16 | 2 | 3 | 2 | 5074.55 | −75.78 | |
| 6Y84 | 3WL | 20 | 1 | 2 | 1 | 3068.30 | −73.94 | |
| Nsp3 | 6W02 | APR | 6 | 2 | 1 | 1 | 2247.84 | −119.05 |
| Nsp6 | DN | K22 | 25 | 3 | 1 | 1 | 2364.82 | −75.26 |
| DN | 27 | 4 | 1 | 1 | 3692.30 | −76.86 | ||
| Nsp9 | 6W4B | AG7 | 13 | 2 | 3 | 1 | 2740.53 | −97.41 |
| Nsp12-Nsp7-Nsp8 | 7BV2 trimer | ATP (ortho) | 79 | 1 | 2 | 1 | 4397.28 | −94.18 |
| POO/ PFI (allo) | 2 | 1 | 1 | 3545.24 | −97.80 | |||
| 77Z (allo) | 1 | 4 | 2 | 4397.28 | −85.22 | |||
| Nsp13 | HM | ADP (ortho) | 40 | 3 | 2 | 2 | 4359.36 | −79.98 |
| 4VA (allo) | 5 | 10 | 5 | 2526.96 | −74.28 | |||
| Nsp14-Nsp10 | HM dimer | SAH | 49 | 2 | 9 | 4 | 5307.98 | −80.25 |
| SAM | 2 | 2 | 1 | 5307.98 | −88.09 | |||
| G3A | 2 | 1 | 1 | 5307.98 | −119.09 | |||
| Nsp15 | 6W01 hexamer | U3P | 170 | 5 | 3 | 1 | 2792.58 | −80.39 |
| 6VWW dimer | U3P | 52 | 6 | 1 | 3 | 2275.76 | −81.75 | |
| Nsp16-Nsp10 | 6WKS dimer | SAM | 63 | 1 | 8 | 1 | 4772.88 | −88.43 |
| GTA | 1 | 1 | 1 | 4772.88 | −118.80 | |||
| 6W4H dimer | SAM | 31 | 1 | 1 | 1 | 3243.06 | −87.81 | |
| GTA | 1 | 2 | 1 | 3243.06 | −112.33 | |||
| N-protein | 6M3M | C5P, 5GP, U5P, AMP, P34 | 7 | 3 | 2 | 2 | 1252.56 | −66.69 |
| 6VYO | 7 | 3 | 3 | 3 | 1961.99 | −70.57 | ||
| PL-Pro | 6W95 | TTT | 23 | 3 | 2 | 1 | 2134.23 | −94.17 |
| SPIKE–ACE2 | 6LZG dimer | YMZ | 56 | 2 | 2 | 1 | 4792.66 | −80.66 |
| 6M0J dimer | 58 | 1 | 5 | 1 | 4407.92 | −74.29 | ||
| 6M17 hexamer | 275 | 1 11 |
1 1 |
1 2 |
3767.99 | −81.79 | ||
| 6VW1 dimer | 61 | 1 | 2 | 1 | 4920.74 | −77.78 | ||
| Correctly Identified Pockets | 20 | 18 | 30 | |||||
| Correct Pockets Ranked as #2 | 9 | 10 | 5 | |||||
| Correct Pockets Ranked as #3 | 6 | 5 | 3 | |||||
| Correct Rockets Out of the Podium | 5 | 7 | 2 | |||||
| Average Rank | 2.18 | 2.43 | 1.45 | |||||
| Precision | 0.5 | 0.45 | 0.75 | |||||
| Accuracy | 0.97 | 0.97 | 0.99 | |||||
| MCC | 0.48 | 0.43 | 0.74 | |||||