Flexible ligand–flexible protein docking in protein kinase systems

Quite a few reviews on molecular docking have already appeared. This mini-review focuses on methods that incorporate protein flexibility in docking rather than those that treat protein targets as rigid molecules. This is still a challenging problem but there are encouraging recent advances. These methods will be reviewed particularly in light of their applications to protein kinases and phosphatases. In addition to obtaining correct docking pose, recent developments on exploring docking pathways are also highlighted.