||Accurate modeling of ligand-binding-site structures plays a critical role in structure-based virtual screening. However, the structures of the ligand-binding site in most predicted protein models are generally of low quality and need refinements. In this work, we present a ligand-binding-site structure refinement protocol using molecular dynamics simulation with restraints derived from predicted binding site templates. Our benchmark validation shows great performance for 40 diverse sets of proteins from the Astex list. The ligand-binding sites on modeled protein structures are consistently refined using our method with an average C alpha RMSD improvement of 0.90 angstrom. Comparison of ligand binding modes from ligand docking to initial unrefined and refined structures shows an average of 1.97 angstrom RMSD improvement in the refined structures. These results demonstrate a promising new method of structure refinement for protein ligand-binding-site structures.