A system, device, and method for predicting a docked position of a target ligand in a binding site of a biomolecule is disclosed. The prediction makes use of a template ligand-biomolecule complex structure in order to predict a target ligand-biomolecule complex structure. The system and device contain modules allowing for the prediction of a target-ligand biomolecule complex structure. A preparation module can receive information identifying a target ligand and a template ligand-biomolecule structure. A pharmacophore matcher module can identify common pharmacophores between the template ligand and the target ligand. A docking module can predict a docked ligand position of the target ligand by overlapping the pharmacophore models of the target ligand and template ligand while the template ligand is in the binding site of the biomolecule. A biomolecule modification module can modify the biomolecule to reduce clashes between the docked target ligand and the biomolecule.