Algorithms for Molecular Biology

Table 1 Number of RMSD computations for the 4state_reduced decoy dataset with varying RMSD threshold.

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

Decoy set	t = 2.4 Å	t = 2.8 Å	t = 3.2 Å	t = 3.6 Å	$\frac{N (N - 1)}{2}$
1ctf	87,219	103,780	122,095	140,094	198,765
1r69	130,510	150,415	171,407	189,659	228,150
1sn3	106,523	124,587	147,101	174,527	217,470
2cro	183,135	206,133	189,277	221,219	227,475
3icb	130,653	119,774	139,425	176,184	213,531
4pti	106,581	131,345	175,432	191,091	236,328
4rxn	95,306	117,515	143,481	190,997	228,826
Total	839,927	953,549	1,088,220	1,283,751	1,550,545

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