Abstract: Molecular docking is a powerful tool for predicting both the binding mode and the binding free energy of a protein-ligand complex. The method was originally developed for the drug discovery, and it can also be used for studies in other fields. Here, current molecular docking methods were carefully reviewed, and a widely-used docking-based virtual screening technology was introduced. Then, applications of molecular docking to the fields of protein engineering, bioremediation, biosensor, nanoscience were presented. This review can promote the applications of molecular docking in studies other than the drug discovery.