Overview of PharmDock. The inverse triangle shows that with progress in the overall docking process, the number of feasible binding poses of a ligand will be reduced. The overall docking process contains the following subsequent steps: Poses sampling: PharmDock samples binding poses by enumerating all possible multiple-points matches between the pre-generated ligand and protein-based pharmacophores and subsequent alignment of common features. Poses ranking: The sampled binding poses are then ranked using a simple pharmacophore-based scoring function (equation 1) to select top ranked poses for subsequent optimization. Both Poses Sampling and Poses Ranking are based on the representation of potential interactions as potential pharmacophores. Poses optimization: The top ranked binding poses will be locally optimized within the protein binding site to generate the final prediction of ligand binding pose and binding score.