Table 1.

Summary of three categories of peptide docking methods

Category	Flexibility	Description	Examples
Template docking	None or little	Use sequence-based homology model to predict docking poses	GalaxyPepDock
Ensemble docking	Conformation ensemble	Prepare a conformation ensemble to describe peptide flexibility and then dock the conformations back into receptor	HPepDock MDockPep pepATTRACT
De novo method	Fully flexible	Model peptide flexibility with the respect to the receptor	ADCP AnchorDock CABS-Dock FlexPepDock HADDOCK