1) Rosetta FlexPepDock is a high-resolution peptide docking (refinement) protocol, implemented within the Rosetta framework. The input for this server is a PDB file of a complex between a protein receptor (first chain) and an estimated conformation for a peptide (second chain). FlexPepDock was shown to be able to accurately refine the peptide structure starting from up to 5.5A RMSD of the native conformation, allowing full flexibility to the peptide and side-chain flexibility to the receptor.
2) Autodock. Autodock itselft as well as PSO@Autodock can be used to dock small peptides on a protein.
3) eHiTS. See also
4) ICM-Dock. Flexible peptide-receptor docking.
A useful link listing many of the docking programs and their capabilities can be found here.
If you happen to know of more programs please let us know!