Table 1.

Test set used in this study

Protein	Small ligand-bound structure			Peptide-bound structure		RMSD (Å)b
	System	PDB	Ligand	PDB	Ligand	Cα atoms	All atoms
MDM2	T-1	1RV1	IMZ	1YCR	p53 TDa	0.87	1.56
	T-2	1T4E	DIZ			0.78	1.35
	T-3	3JZK	YIN			0.75	1.44
	T-4	3LBK	K23			0.74	1.42
MDMX	X-1	3LBJ	WW8	3DAB	p53 TD	0.59	1.41
					Avg.	0.75	1.44

^aTransactivation domain peptide.

^bRMSD of the binding-site residues in the small ligand-bound receptor to those in the peptide-bound receptor; the binding-site residues are defined by a distance cut of 4 Å from any atoms of the small ligand.