Table 2.
Performance of benchmarking detection methods for holo proteins in terms of: (d) distance (FN) false negatives to PDBsum ground-truth cavity centers; (TP) true positives; (FP) false positives; (TN) true negatives; (S v) sensitivity; (S c) specificity; (a) accuracy; (r d) ratio of detected ground-truth cavities; and (C u) cumulative number of undetected ground-truth cavities
| d | GaussianFinder | ConCavity | POCASA | SURFNET | PASS | GHECOM | Fpocket | 3V | KVFinder |
|---|---|---|---|---|---|---|---|---|---|
| d∈[0.0,1.0] | 16081 | 3133 | 5234 | 3668 | 11738 | 10438 | 14063 | 9174 | 12493 |
| d∈]1.0,2.0] | 366 | 239 | 338 | 2574 | 2100 | 571 | 432 | 703 | 719 |
| d∈]2.0,3.0] | 410 | 296 | 419 | 1063 | 281 | 789 | 406 | 811 | 813 |
| d∈]3.0,4.0] | 334 | 488 | 609 | 925 | 360 | 932 | 504 | 349 | 418 |
| TP | 17191 | 4156 | 6600 | 8230 | 14479 | 12730 | 15405 | 12049 | 14443 |
| FP | 2460 | 2155 | 2083 | 1806 | 634 | 1278 | 2151 | 1564 | 1941 |
| TN | 3231 | 916 | 2673 | 1559 | 4080 | 4968 | 3423 | 2476 | 2725 |
| FN | 440 | 362 | 214 | 227 | 207 | 658 | 391 | 511 | 553 |
| S v | 0.975 | 0.919 | 0.969 | 0.973 | 0.986 | 0.951 | 0.975 | 0.959 | 0.963 |
| S c | 0.568 | 0.298 | 0.562 | 0.463 | 0.866 | 0.795 | 0.614 | 0.612 | 0.584 |
| a | 0.876 | 0.668 | 0.801 | 0.828 | 0.957 | 0.901 | 0.881 | 0.875 | 0.873 |
| r d | 0.963 | 0.233 | 0.369 | 0.461 | 0.811 | 0.713 | 0.863 | 0.675 | 0.809 |
| C u | 659 | 13694 | 11250 | 9620 | 3371 | 5120 | 2445 | 5801 | 3407 |