Fast structure similarity searches among protein models: efficient clustering of protein fragments

Table 3 Fragment clustering.

RMSD threshold (Å)	N. struct.	This work	$\frac{N (N - 1)}{2}$	ratio	Rep. Struct.
0.05	107,184	57,978,627	5,744,151,336	0.0100	79,994
0.1	79,994	28,610,140	3,199,480,021	0.0089	47,502
0.2	47,502	19,089,084	1,128,196,251	0.0169	13,066
0.4	13,066	4,479,481	85,353,645	0.0525	1,853
0.8	1,853	393,824	1,715,878	0.2295	131
Total	107,184	110,551,156	5,744,151,336	0.0193

Columns report the threshold RMSD chosen for clustering, the number of starting fragments, the number of RMSD computations done, the number of computations in an all-vs-all comparison, the number of representative fragments, used as starting fragments at the next iteration. CA atoms have been used for superposition.

ISSN: 1748-7188