Table 2.

FEATURE benchmark of the 20 apo-holo pairs of calcium-binding proteins

Protein and calcium ID	Holo structure	Apo structure	Apo-gap	Apo-loop
1B9AA110	81.72	26.75	5.41	51.58
1C1R_247	56.57	51.71	1.94	55.43
1DPO_246	52.89	47.94	-0.17	50.87
1DVIB275	66.89	10.63	0.00	29.70
1DVIB277	68.39	57.51	-18.90	41.18
1F6SB202	68.11	54.04	16.58	54.46
1HAZB1246	51.82	48.21	-4.82	32.72
1I40A305	30.52	27.87	16.92	46.64
1K94_998	80.71	63.46	-22.81	42.92
1K94_999	40.31	32.63	-0.45	50.96
1K96A91	79.61	45.63	9.77	59.27
1KXQB4003	54.99	43.25	22.01	59.53
1NLS_240	61.98	52.09	28.46	60.76
1NOL_632	36.88	30.22	30.22	41.85
1PSH_1	34.09	33.81	22.03	56.37
1QMDA403	60.45	30.41	27.37	50.41
1QMDA405	59.81	45.00	37.05	52.09
2POR_304	47.41	71.34	34.96	89.29
3LHM_131	61.69	54.34	2.46	58.95
5CHY_401	50.19	46.70	23.56	54.08

We compare the performance of FEATURE on the holo structures, the apo structures, the apo structures of which the binding loops were removed (apo-gap), and the apo structures of which the binding loops (apo-loop) have been rebuilt using modeling methods. Protein and calcium ID are from PDB (column 1). FEATURE scores that evaluate the probability of the likelihood of a site being calcium-binging are listed in column 2-5. Of the 20 pairs, 17 apo-loops have higher FEATURE scores than the corresponding apo structures. Bolded number indicates that FEATURE identifies the calcium-binding site correctly using a score threshold of 50. FEATURE identifies 15 out of 20 calcium-binding sites in the holo structures. Combined with modeling methods, FEATURE identifies 14 out of 20 calcium-binding sites in the apo-loops. For comparison, FEATURE identifies binding sites correctly in only 7 out of 20 the apo structures, and 0 out of 20 the apo-gaps. These results demonstrate that reconstruction of the calcium-binding loops in the apo structures allows FEATURE to identify cryptic calcium sites effectively.