Template-based molecular docking Sometimes known as template-based or homology modelling, template-based docking is a computer technique used in molecular docking to predict the three-dimensional arrangement of a protein-ligand complex by using the established structure of a comparable protein-ligand complex ( ). This method is predicated on the idea that proteins with similar sequences or structures often bind similarly to ligands. Matching the sequence or structure of the target protein with that of the template protein models the structure of the target protein in template-based docking. To create the missing or variable elements, one then uses computational methods, including side-chain prediction or loop modelling. Molecular docking techniques are applied to anticipate the binding shape and affinity of ligands within the binding site of the target protein once a model of the protein is generated ( ).