Table 3.

Some basic methods for including receptor flexibility.

Method	Description	Advantage	Disadvantage	Program
Soft potential	Change vdW to allow for overlap between receptor and ligand atoms	Computational efficiency. Easy to implement and use combined with other methods.	Inadequate flexibility. Describe flexibility in an implicit, rude and non- quantitative way.	GOLD [65] AutoDock [31]
Rotamer library	Search side chain library to obtain possible conformations	Relative computational efficiency. Avoid minimization barriers.	Strong dependence on the database used. No backbone flexibility.	ICM [61]
Receptor side chain flexibility	Sample both side chain and ligand conformations simultaneously using GA	Relative computational efficiency. Model the effect that ligand make on binding site residues.	Only selected side chains are involved. No backbone flexibility.	AutoDock 4 [112]
Ensemble of protein conformations	Docking ligand to a series of receptor structures which represent different conformational states.	Include full and explicit flexibility.	Expensive computational cost. Limited by protein conformations used in sampling.	DOCK [113] FlexE [38]