Table 4

Fragment clustering on backbone.

RMSD threshold (Å)

N. struct.

This work

<a onClick="popup('http://www.almob.org/content/7/1/16/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.almob.org/content/7/1/16/mathml/M1">View MathML</a>

ratio

Rep. Struct.


0.05

107,184

53,793,796

5,744,151,336

0.0094

105,299

0.1

105,299

124,506,221

5,543,887,051

0.0225

87,195

0.2

87,195

57,001,567

3,801,440,415

0.0150

63,829

0.4

63,829

65,723,340

2,037,038,706

0.0322

21,637

0.8

21,637

33,375,313

234,069,066

0.1426

2,445

1.6

2,445

2,586,436

2,987,790

0.8657

33

3.2

33

528

528

1.0000

2


Total

107,184

336,987,202

5,744,151,336

0.0587


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. Atoms N, CA, C, O have been used for superposition.

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

Open Data