Table 1.

Clustering by structural similarity of the 1,000 lowest energy conformations in the Park–Levitt sets

Protein	rmsd cutoff	Cluster size	rmsd center to native (rank in proximity to native state)	rmsd lowest energy conformation	Mean rmsd of ensemble
2cro	4 Å	44	4.7  (44)	5.6	8.8
	5 Å	85	3.2
	6 Å	151	6.7
1ctf	4 Å	69	1.7  (2)	2.0	8.1
	5 Å	132	2.9
	6 Å	247	2.9
1r69	4 Å	45	3.3  (12)	5.2	8.0
	5 Å	129	4.2
	6 Å	257	3.9
3icb	4 Å	51	1.7  (1)	4.7	9.2
	5 Å	83	2.0
	6 Å	137	1.7
1sn3	4 Å	18	8.1  (417)	2.1	8.4
	5 Å	40	7.2
	6 Å	120	6.9
4pti	4 Å	22	2.5  (10)	10.0	9.2
	5 Å	44	5.0
	6 Å	100	6.1
1ubq	4 Å	52	2.0  (3)	5.3	9.2
	5 Å	94	2.0
	6 Å	154	3.7
4rxn	4 Å	36	3.1  (13)	8.4	8.4
	5 Å	82	3.2
	6 Å	153	5.4