Table 1.

Comparison of experimental and theoretical complexes investigated

	Dissociation constant (KD)	Experimental interface SASA (Å2)	Theoretical interface SASA (Å2)	rmsd (Å)
EIN/HPr	6 μMa	1948	2203	1.6
Barnase/Barstar	0.2 pMb	1556	1368	0.79
Tom20/Presequence	20 μMc	1000	1000	0.54
Cyt c/Ccp	≈μMd	1140	1670	2.2

The experimental protein–protein interaction interface observed in the X-ray or NMR structure of each complex is compared with those obtained using our restrained soft-docking approach. The theoretical interface calculations for each complex were determined using the protein–protein interaction server developed by Prof. Janet Thornton and Dr. S. Jones (http://www.biochem.ucl.ac.uk). The rmsd of the backbone trace between the experimental structure and our best solution for each complex is included.^a Garrett et al. 1999; ^bBuckle et al. 1994; ^cAbe et al. 2000; ^dPelletier and Kraut 1992.