The A* search is repeated for each partial conformation of docked seed fragments until all have been considered for reconstruction into a different docked conformation of the original compound. A final energy minimization procedure is performed on the protein-ligand complex treating the protein as fully flexible (side-chain and backbone) to remove steric clashes in the process of growing the ligand into the binding site. In addition to knowledge-based and molecular mechanics energy minimization, the fragment reconstruction process intrinsically accounts for ligand flexibility in the docking process. The described protocol results in a ranked list of docked and minimized protein-compound complexes.