Table 3 Average molecular properties of reference ligands and generated molecules for the PDBbind dataset
From: Target-aware 3D molecular generation based on guided equivariant diffusion
Metrics | Ref. | ResGen | PocketFlow | GCDM | TargetDiff | DiffSBDD | PMDM | DiffGui |
|---|---|---|---|---|---|---|---|---|
Vina Score (↓) | − 7.747 ± 3.56 | − 2.177 ± 1.68 | − 3.596 ± 1.80 | − 2.095 ± 1.29 | − 5.263 ± 2.54 | − 5.011 ± 2.28 | − 4.990  ± 2.41 | − 6.700 ± 2.55 |
Vina Min (↓) | − 8.605 ± 2.44 | − 4.704 ± 2.16 | − 4.823 ± 1.85 | − 3.545 ± 1.49 | − 6.959 ± 2.58 | − 5.894 ± 2.22 | − 6.516 ±2.61 | − 7.655 ± 2.51 |
Vina Dock (↓) | − 9.133 ± 2.14 | − 7.154 ± 2.29 | − 6.245 ± 2.00 | − 5.130 ± 1.66 | − 8.195 ± 2.23 | − 6.853 ± 2.03 | − 7.577 ± 2.54 | − 8.448 ± 2.24 |
QED (↑) | 0.459 ± 0.22 | 0.577 ± 0.15 | 0.501 ± 0.17 | 0.477 ± 0.13 | 0.460 ± 0.22 | 0.466 ± 0.19 | 0.474 ± 0.21 | 0.631 ± 0.21 |
SA (↑) | 0.720 ± 0.10 | 0.784 ± 0.11 | 0.784 ± 0.15 | 0.706 ± 0.13 | 0.604 ± 0.13 | 0.633 ± 0.13 | 0.607 ± 0.15 | 0.678 ± 0.15 |
LogP | 1.731 ± 2.74 | 1.749 ± 1.88 | 2.855 ± 1.80 | 0.807 ± 1.67 | 1.707 ± 2.38 | 1.384 ± 2.02 | 1.515 ± 2.60 | 1.977 ± 3.01 |
TPSA | 115.91 ± 69.43 | 60.11 ± 29.91 | 38.46 ± 45.58 | 53.45 ± 34.28 | 103.06 ± 60.60 | 85.66 ± 45.87 | 117.74 ± 130.83 | 100.49 ± 62.97 |
