Target | RMSD (Ã…) of the best best-pose | RMSD (Ã…) of the best top-rank pose | Reasons for incorrect ranking | Due to the scoring functions? | Possible recommendations |
---|---|---|---|---|---|
cp3a4 | 2.03 Surflex | 4.14 Glidescore | Coordination bond | No | Â |
xiap | 1.25 Surflex | 3.78 FlexX | Ligand not well anchored in the binding site | No | Â |
hdac8 | 0.91 Glidescore | 2.91 Goldscore | The metal ion chelation is not considered explicitly or not well parametrized | Yes | With modified parameters of the metal, the top-rank pose is correct |
hs90a | 0.32 Gold | 9.54 Glidescore, FlexX, Goldscore | An off-center pose is privileged | No | Possibility of the existence of a secondary site difficult to reach (dynamical considerations) |
igf1r | 0.72 Surflex | 2.32 Surflex | Difference in protonation | No | Include in situ protonation in the docking procedure |
cxcr4 | 1.94 Gold | 2.95 Surflex | Difference in protonation | No | Similar to igf1r |
pnph | 0.65 Gold | 3.14 Glidescore | Difference in protonation | No | Similar to igf1r |
hivpr | 1.97 Surflex | 2.26 Glidescore, Goldscore | The difference is located in a loose or exposed to solvent part of the ligand | No | The difference is not a problem |
tysy | 1.27 Surflex | 2.7 Goldscore | The difference is located in a loose or exposed to solvent part of the ligand | No | Similar to hivpr |