This approach combines the conformational information gained from MD with ligand docking and accounts for the dynamic movement of both protein and ligand.
Although some docking methods accounting for protein flexibility exist, most large scale virtual screening approaches work with rigid protein models.
Standard docking cannot account for such induced fit phenomena, so that likely many of the resulting poses do not correspond to the true binding mode of the respective ligands.
Even if we accept that we judge Kipling more harshly because he feels closer to us, that still doesn't quite explain the obligation everyone feels to place him in the dock and account for his racial politics.
Currently, most docking programs do not account for the presence of halogen bonding in their scoring functions.
However, most docking program don't account for halogen bonding in their scoring functions and are not able to utilize this new approach.
On that account, molecular docking holds a great promise to speed up drug discovery, thus it is widely used as an integral part of many currently ongoing drug development projects.
In order to avoid over-interpreting small changes in the docking performance and to account for the heuristic nature of the docking tools, we defined the "safety margin" of ±0.05 ΔpROC-AUC N below which it is considered non-significant in the normalization task.
> Crystallographic water molecules were taken into account for docking calculations.
Taking the fourfold symmetry of the receptor into account, blind docking established five distinct putative binding sites.
