In many cases the binding site of a ligand with its target is known from experiments before docking approaches are used. In this case, the search space can be limited when looking for therapeutic ligands. As a consequence, the speed of screening is enhanced. In other cases, a therapeutic ligand shows good effects on the target but no or limited structural information of that target is available, especially in the presence of the ligand. Consequently, novel strategies of how to approach this issue with existing software is of need.
Up to nine putative therapeutic ligands are used in various docking protocols, which also includes the application of different docking software, searching for unknown binding sites on the target. The target is the viral channel forming protein (viroporin) p7 of hepatitis C virus. Protein p7 consists of two transmembrane domains separated by a short loop. In its functional form it is shown to exist genotype dependent as a homo hexamer or heptamer. The protein is vital to the survival of the virus.