Table II.

Docking Rigid Ligand Conformations to their Native (Bound) Structures (Self-Docking and Cross-Docking)

		Peptide		RosettaLigand
Protein	PDB code	Class	Sequence	RMSD (Å)a	Ebind (kcal/mol)	DRUGSCORECSDEbind (kcal/mol)b
PSD-95	1BE9	I	KQTSV	0.70	−13.21	−195.32
		II	EYLGLDVPV	2.07	−14.26	−213.24
GRIP	1N7F	I	KQTSV	0.90	−15.33	−153.86
		II	ATVRTYSC	0.90	−21.96	−256.95
Syntenin	1OBX	I	DSVF	0.37	−15.83	−183.48
		II	NEFYA	0.60	−17.73	−187.15
	1OBY	I	DSVF	0.80	−14.32	−184.83
		II	NEFYA	0.56	−22.44	−269.06
Erbin	1N7T	I	TGWETWV	0.83	−16.50	−232.20
		II	EYLGLDVPV	2.0	−11.56	−177.19
	1MFG	I	TGWETWV	0.67	−15.07	−196.94
		II	EYLGLDVPV	0.35	−21.71	−308.70

^aRMSD values between the top scoring pose in Ångstroms measured over all heavy atoms of the peptide and the peptide's position in the crystal structure.

^bCalculated with DrugScore online (http://pc1664.pharmazie.uni-marburg.de/drugscore/). Higher negative values indicate a higher-affinity prediction.