Yannick van Dijk

Thanks for your quick answers! I see what you mean. However, I think this will not work for this case because of the covalent docking mode. If I would refine the pose, the link atom will be dangling somewhere it should not be. This is the reason why we kept the pose as is. Keeping it this way, the linkatom (both present in the protein and ligand) would remain at the same position for every generated pose from GOLD. Our hypothesis was that keeping the pose as is would then result in a systemic error....

I don't know if I understand you correctly. I am using smina to rescore the poses that I have. I have obtained the poses using GOLD. These poses were thus minimized by GOLD already. We are not using any flexibility for the protein except for hydrogen rotation. Smina is used as an extra scoring function outside the GOLD scoring function package to check whether it could give a better ranking as compared to experimental data.

Dear David Koes, I have a couple of pose solutions in which a link atom is present in both protein and ligand having exactly the same coordinates (In this case a S from a CYS residue). I have rescored the solutions using smina with the flag --score_only. I chose to not use the quasi-covalent mode from smina because all my poses have exactly this overlap. My thought was that this overlap would be a systemic error and would not affect the relative ranking of poses. Scores could be obtained without...

Dear David Kroes, I have a couple of pose solutions in which a link atom is present in both protein and ligand having exactly the same coordinates (In this case a S from a CYS residue). I have rescored the solutions using smina with the flag --score_only. I chose to not use the quasi-covalent mode from smina because all my poses have exactly this overlap. My thought was that this overlap would be a systemic error and would not affect the relative ranking of poses. Scores could be obtained without...