TABLE 2.

Overall averages of RMSD of conserved residues and nonconserved residues for all complexes

		Complex simulations		Monomer simulations
PDB ID	Chain	C	NC	C	NC
Homodimers
1bft	A	2.00	1.65	3.46	2.95
	B	1.97	2.11	2.39	2.70
1bzd	A	1.96	1.56	2.41	1.90
	B	1.87	1.66	2.11	1.93
1cd0	A	2.92	3.42	2.33	2.27
	B	3.28	3.61	2.71	3.44
1cqk	A	1.70	2.58	2.02	2.74
	B	1.61	2.48	2.34	2.97
1mr8	A	2.07	2.41	2.48	2.33
	B	2.10	2.37	3.01	3.38
1x2i	A	1.18	1.76	2.72	4.22
	B	1.65	1.87	3.64	3.65
Average		2.06	2.56	2.66	3.12
SD		0.66	0.61	0.47	0.63
Antibody-antigen
1ddh	A	1.60	1.92	2.26	1.92
	P	—	—	—	—
1fcc	A	1.41	1.6	1.87	2.42
	C	—	—	—	—
1qnz	H	1.36	1.67	1.41	2.20
	P	—	—	—	—
1vfb	B	—	—	—	—
	C	1.09	2.02	2.38	2.99
Average		1.36	1.80	1.98	2.39
SD		0.18	0.17	0.38	0.39
Enzyme-inhibitor
1bjr	E	1.61	1.91	1.68	1.93
	I	—	—	—	—
1sbw	A	2.48	2.66	2.24	2.41
	I	—	—	—	—
1ugh	E	2.04	2.78	2.78	3.36
	I	—	—	—	—
2sni	E	1.56	2.04	1.99	2.70
	I	—	—	—	—
1cjq	A	—	—	—	—
	B	3.81	4.24	1.95	2.79
Average		2.30	2.73	2.13	2.64
SD		0.83	0.83	0.37	0.47

C, conserved residue; NC, nonconserved residue. The results of the complex and monomer simulations are given.