From: How accurate and statistically robust are catalytic site predictions based on closeness centrality?
Avg.#/PDB | Total accuracy2 | Per PDB accuracy3 | p-value4 | TP & FP rate5 | TP:FP ratio | 1 correct per PDB6 | 1 correct expect7 |
---|---|---|---|---|---|---|---|
(a.) Raw CC values (no filter) | |||||||
1.3 | 6.0 | 2.7 (10.8) | 2.7E-09 | 2.1/0.4 | 6.0 | 7.6 | 1.1 |
2.4 | 6.8 | 4.2 (11.6) | 2.8E-22 | 4.9/0.7 | 7.2 | 15.0 | 2.0 |
3.6 | 6.5 | 4.5 (10.6) | 2.4E-30 | 7.0/1.0 | 6.9 | 19.9 | 3.1 |
4.6 | 6.3 | 4.7 (10.0) | 2.4E-37 | 8.8/1.3 | 6.9 | 23.4 | 3.9 |
5.7 | 6.3 | 4.9 (9.6) | 9.4E-47 | 11.0/1.6 | 6.9 | 27.6 | 4.8 |
(b.) Solvent accessibility filter | |||||||
1.1 | 14.2 | 7.5 (17.4) | 2.8E-42 | 5.3/0.3 | 18.7 | 15.9 | 1.0 |
2.2 | 13.0 | 9.2 (16.8) | 7.5E-72 | 9.7/0.6 | 16.9 | 25.4 | 1.9 |
3.3 | 11.1 | 8.7 (14.7) | 6.8E-82 | 12.2/0.9 | 14.2 | 29.3 | 2.9 |
4.4 | 10.8 | 8.9 (13.2) | 4.5E-103 | 15.8/1.2 | 13.7 | 36.7 | 3.9 |
5.4 | 10.4 | 8.9 (12.4) | 2.7E-120 4 | 18.8/1.4 | 13.2 | 41.3 | 4.8 |
(c.) Residue identify filter | |||||||
1.1 | 22.4 | 11.3 (21.0) | 3.8E-83 | 8.3/0.3 | 32.6 | 23.0 | 1.0 |
2.2 | 19.6 | 13.5 (19.8) | 8.8E-134 | 14.5/0.5 | 27.6 | 35.7 | 1.9 |
3.2 | 17.9 | 13.8 (18.2) | 0.0 | 19.2/0.8 | 24.7 | 42.8 | 2.8 |
4.3 | 17.6 | 14.3 (17.0) | 0.0 | 25.0/1.0 | 24.1 | 50.5 | 3.7 |
5.2 | 16.5 | 13.9 (156.3) | 0.0 | 29.3/1.3 | 22.4 | 56.2 | 4.7 |
(d.) Combination filter (solvent accessibility + resodue identify) | |||||||
1.1 | 25.2 | 12.9 (21.8) | 0.0 | 18.6/0.5 | 39.0 | 26.1 | 1.0 |
2.1 | 20.7 | 14.4 (20.7) | 0.0 | 31.0/1.0 | 30.8 | 36.7 | 1.9 |
3.1 | 17.9 | 13.5 (17.1) | 0.0 | 39.9/1.5 | 26.2 | 44.2 | 2.7 |
4.1 | 15.9 | 12.8 (14.6) | 0.0 | 45.4/2.1 | 21.8 | 49.8 | 3.6 |
5.2 | 13.9 | 11.7 (13.1) | 0.0 | 50.0/2.7 | 18.7 | 53.0 | 4.6 |