Table 3

Fragment clustering.

RMSD threshold (Å)

N. struct.

This work

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.

Fogolari et al. Algorithms for Molecular Biology 2012 7:16   doi:10.1186/1748-7188-7-16