TABLE 1.

Summary of the results of using the singlewise score function to calculate a near-native conformation of rhodopsin and the three bacterial rhodopsins, bacterio-, halo- and sensory rhodopsin II

Protein	RMSd of randomly generated conformations (± SD) Å	RMSd of the highest-score conformation from the native-state structure (Å)	Percentile of highest-scoring conformation
Bacteriorhodopsin	3.9 ± 0.4	3.2	5.6
Halorhodopsin	3.3 ± 0.4	2.5	4.2
Sensory rhodopsin II	3.5 ± 0.4	1.8	0.01
Rhodopsin	4.5 ± 0.4	3.7	3.5

The three bacterial proteins are related to one another in terms of sequences and structures, but show some local structural differences. Rhodopsin is different in terms of architecture and sequence. Templates for the three bacterial rhodopsins were constructed on the basis of their high-resolution PDB structures. Rhodopsin's templates were constructed on the basis of helix-axes parameters (Baldwin et al., 1997) taken from its 9-Å in-plane resolution structure (Unger et al., 1997). Percentiles were computed on the basis of a distribution of expected RMSd values for each protein (see Results). In all cases, the best-scoring conformation is significantly closer to the native state than predicted by chance.