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.
