Calibur: a tool for clustering large numbers of protein decoys

BMC Bioinformatics

Table 3 Total scores and CPU times.

Sample size	Average TM-score		Total C_αRMSD		Total CPU Time (s)
	SPICKER	Calibur	SPICKER	Calibur	SPICKER	Calibur
1000	0.571107	0.578102	291.534	281.994	136.05	237.25
2500	0.574379	0.578386	284.937	286.09	687.45	746.84
4000	0.576045	0.576859	284.953	284.108	1851.34	1533.81
5500	0.574475	0.57845	284.18	283.055	3276.36	2781.55
7000	0.576323	0.578823	284.927	278.769	7029.09	4320.95
8500	0.57843	0.580889	283.325	279.248	8132.9	5906.61
10000	0.577543	0.581236	282.919	279.1	10745.5	7822.75
11500	0.578748	0.582175	282.644	281.192	14293.8	10374.2
13000	0.578432	0.582425	283.795	281.701	16608.8	12420.5

Average TM-score and total C_αRMSD for the best decoys obtained, as well as the total CPU time used, on the sampled sets of sizes 1000, 2500, 4000, 5500, 7000, 8500, 10000, 11500, 13000. (SPICKER requires additional pre-processing of the input PDB files which are not added into the CPU times here.)

ISSN: 1471-2105