Example of results obtained by confined docking protocol. (A) All protein-based pharmacophores identified based on protein structure of factor Xa (PDB: 1MQ6) without inclusion of information about known active ligands. The protein surface is colored as grey. Protein-based pharmacophores are shown as lines for hydrogen bond donor/acceptor and small green spheres for hydrophobic elements. (B) A subset of the protein-based pharmacophores selected from (A) with the consideration of three known active ligands. The X-ray binding poses of known ligands are shown in stick representation. (C) Ligand binding poses predicted by PharmDock for co-crystallized ligand in PDB structure 1MQ6. Orange: Ligand binding pose predicted in the unbiased docking setting with all identified protein-based pharmacophores. Green: Ligand binding pose predicted with the selected pharmacophores showing excellent agreement (1.8 Å RMSD) with the X-ray pose (yellow ligand in B).