TABLE 2.
Summary of results from both ideal and nonideal tests
| Nonideal test result
|
||||||||
|---|---|---|---|---|---|---|---|---|
| Ideal test result
|
Test 1
|
Test 2
|
||||||
| PDB codes | Mode No. (overlap) | Pool size | No. pairs | Overlap | No. pairs | Overlap | No. pairs | Overlap |
| 8adh 6adh | No. 3(0.680) | 49 | – | – | – | – | – | – |
| 10 | 0.564 | 8 | 0.622(0.100) | 10 | 0.528(0.081) | |||
| 4 | 0.300 | |||||||
| 1avr 1avh | No. 2(0.412) | 14 | 2 | 0.538 | 9 | 0.423(0.134) | – | – |
| 3 | 0.550 | 9 | 0.423(0.134) | 1 | 0.406(0.000) | |||
| 3 | 0.455 | |||||||
| 4dfr 5dfr | No. 1(0.611) | 9 | – | – | – | – | – | – |
| 2 | 0.588 | 9 | 0.390(0.000) | 3 | 0.297(0.308) | |||
| 1 | 0.612 | |||||||
| 1ddt 1mdt | No. 2(0.564) | 147 | 1 | 0.640 | 2 | 0.607(0.067) | 1 | 0.640(0.000) |
| 7 | 0.650 | 9 | 0.646(0.011) | 7 | 0.650(0.000) | |||
| 2 | 0.421 | |||||||
| 3enl 7enl | No. 1(0.345) | 49 | 1 | 0.499 | 8 | 0.366(0.107) | 1 | 0.499(0.000) |
| 10 | 0.500 | 8 | 0.366(0.107) | 10 | 0.500(0.003) | |||
| 1 | 0.346 | |||||||
| 1hhp 1ajx | No. 3(0.70) | 6 | 1 | 0.784 | – | – | – | – |
| 1 | 0.784 | 5 | 0.187(0.069) | 1 | 0.517(0.589) | |||
| 1 | 0.068 | |||||||
| 1lfh 1lfg | No. 1(0.613) | 62 | 1 | 0.671 | 5 | 0.620(0.236) | 1 | 0.671(0.000) |
| 8 | 0.882 | 10 | 0.737(0.170) | 10 | 0.867(0.025) | |||
| 4 | 0.663 | |||||||
| 2lao 1lst | No. 1(0.886) | 40 | 1 | 0.932 | 1 | 0.918(0.028) | 1 | 0.932(0.000) |
| 3 | 0.942 | 10 | 0.937(0.006) | 3 | 0.942(0.000) | |||
| 3 | 0.920 | |||||||
| 3tms 2tsc | No. 4(0.503) | 15 | 4 | 0.563 | 2 | 0.536(0.133) | 4 | 0.556(0.040) |
| 7 | 0.664 | 10 | 0.648(0.025) | 7 | 0.637(0.043) | |||
| 1 | 0.438 | |||||||
| 1ypt 1yts | No. 6(0.470) | 23 | 1 | 0.662 | 1 | 0.626(0.117) | 1 | 0.662(0.000) |
| 9 | 0.759 | 10 | 0.756(0.020) | 9 | 0.754(0.014) | |||
| 1 | 0.383 | |||||||
| 1l3s 1lv5 | No. 5(0.696) | 56 | 5 | 0.704 | – | – | 5 | 0.695(0.044) |
| 7 | 0.719 | 10 | 0.633(0.174) | 7 | 0.710(0.026) | |||
| 6 | 0.103 | |||||||
| 1bpx 1bpy | No. 1(0.710) | 31 | 1 | 0.755 | 3 | 0.756(0.103) | 1 | 0.755(0.000) |
| 7 | 0.759 | 10 | 0.807(0.038) | 8 | 0.759(0.001) | |||
| 1 | 0.711 | |||||||
| 1ih7 1ig9 | No. 2(0.804) | 82 | 1 | 0.815 | 3 | 0.809(0.110) | 1 | 0.815(0.000) |
| 5 | 0.817 | 10 | 0.874(0.017) | 5 | 0.817(0.000) | |||
| 1 | 0.058 | |||||||
| 2ktq 3ktq | No. 4(0.504) | 40 | 1 | 0.755 | 4 | 0.564(0.295) | 1 | 0.755(0.000) |
| 10 | 0.790 | 10 | 0.710(0.167) | 10 | 0.786(0.024) | |||
| 1 | 0.116 | |||||||
| 4q21 5p21 | No. 2(0.494) | 29 | 1 | 0.579 | 8 | 0.499(0.109) | 2 | 0.590(0.047) |
| 10 | 0.660 | 10 | 0.515(0.091) | 9 | 0.615(0.061) | |||
| 3 | 0.191 | |||||||
| 1tag 1tnd | No. 3(0.385) | 49 | 1 | 0.478 | 3 | 0.405(0.185) | 1 | 0.478(0.000) |
| 9 | 0.531 | 10 | 0.572(0.096) | 9 | 0.526(0.012) | |||
| 2 | 0.217 | |||||||
| 9aat 1ama | No. 6(0.515) | 37 | 4 | 0.545 | – | – | – | – |
| No. 7(0.459) | 8 | 0.604 | 9 | 0.505(0.153) | 8 | 0.491(0.100) | ||
| 5 | 0.210 | |||||||
| 1cll 1ctr | No. 5(0.405) | 28 | 1 | 0.695 | 1 | 0.484(0.119) | 1 | 0.695(0.000) |
| No. 4(0.380) | 1 | 0.695 | 8 | 0.578(0.057) | 1 | 0.695(0.000) | ||
| 2 | 0.313 | |||||||
| 1hil 1him | No. 4(0.598) | 13 | 1 | 0.684 | 10 | 0.664(0.198) | – | – |
| No. 1(0.460) | 6 | 0.809 | 10 | 0.664(0.198) | 8 | 0.479(0.384) | ||
| 1 | 0.477 | |||||||
| 1omp 1anf | No. 2(0.675) | 60 | 1 | 0.711 | 3 | 0.765(0.184) | 1 | 0.711(0.000) |
| No. 1(0.650) | 8 | 0.861 | 10 | 0.862(0.069) | 8 | 0.857(0.010) | ||
| 2 | 0.823 | |||||||
| 1dfl 1kk7 | No. 1(0.518) | 102 | 1 | 0.638 | 5 | 0.516(0.217) | 1 | 0.638(0.000) |
| No. 3(0.475) | 10 | 0.813 | 10 | 0.657(0.109) | 10 | 0.800(0.015) | ||
| 1 | 0.518 | |||||||
| 1vom 1mma | No. 1(0.558) | 89 | 1 | 0.734 | 7 | 0.561(0.172) | 1 | 0.734(0.000) |
| No. 2(0.371) | 2 | 0.752 | 10 | 0.618(0.086) | 2 | 0.752(0.001) | ||
| 2 | 0.674 | |||||||
For each test case, the first row shows the minimal number of pairs needed to match the maximal overlap between any single mode and the measured conformational change; the second row shows the number of pairs when the maximal overlap between the computed and the measured conformational changes is obtained. For the two nonideal tests, both the average overlap and its standard deviation (inside parentheses) are shown. For the ideal test, the third row shows the corresponding result for the “hard constraint” method as a comparison.