Template-Based (Homology) Docking Using known protein structures (templates), template-based (homology) Docking is a computer method indispensable in structural biology and drug development that predicts the 3D structure of a target protein and performs molecular binding. This method depends on the idea that proteins with similar sequences usually show identical shapes and activity. Two main phases comprise the process: first, using a 3D model of the target protein derived from sequence comparison for template-based molecular docking, whereby possible ligands are assessed against the projected structure to identify potential drug candidates( ).