TABLE 2.

Summary of results using a modified version of the conformation-sampling method of Monge et al. (1994) in conjunction with the pairwise score function

Protein	Number of structures sampled	Maximal RMSd from native of sampled structures (Å)	RMSd of the highest-score conformation from the native-state structure (Å)	Score rank of the native structure	Correlation coefficient (r) of RMSd values versus pairwise scores
Rhodopsin	109	6.2	1.5	2	−0.78
Bacteriorhodopsin	96	4.0	1.9	30	−0.54
Aquaporin-1	26	3.7	0.9	6	−0.63

The three TM proteins that were tested are heterogeneous in terms of functions, structures, and sequences. The anticorrelations obtained in all three cases demonstrate that the pairwise score is capable of ranking conformations according to their similarity to the native-state structure in a variety of cases.