Table 2.
Comparison of the performance measures of DR_Bind, BindN+, NAPS and DNABINDPROT using the same data set of 83 DNA bounda or 55 DNA-free protein structuresb,c
| Server | DR_Bind | BindN+ | NAPS | DNABINDPROT |
|---|---|---|---|---|
| TP | 728 (419) | 1013 (542) | 328 (180) | 244 (169) |
| FP | 831 (566) | 1798 (1129) | 733 (459) | 1040 (772) |
| TN | 18 128 (11 596) | 17 161 (11 033) | 18 226 (11 703) | 17 919 (11 390) |
| FN | 1362 (792) | 1077 (669) | 1762 (1031) | 1846 (1042) |
| Precision | 0.47 (0.43) | 0.36 (0.32) | 0.31 (0.28) | 0.19 (0.18) |
| Sensitivity | 0.35 (0.35) | 0.48 (0.45) | 0.16 (0.15) | 0.12 (0.14) |
| Specificity | 0.96 (0.95) | 0.91 (0.91) | 0.96 (0.96) | 0.95 (0.94) |
| Accuracy | 0.90 (0.90) | 0.86 (0.87) | 0.88 (0.89) | 0.86 (0.86) |
| mcc | 0.35 (0.33) | 0.34 (0.31) | 0.16 (0.15) | 0.08 (0.09) |
aThe PDB entries are listed in Supplementary Table S1; the total number of residues in the data set is 21 049, out of which 2090 residues are DNA-binding (=TP+FN) and 18 959 residues are non-DNA-binding (=FP+TN).
bPerformance measures based on the DNA-free protein structures are in the parentheses.
cThe PDB entries are listed in Supplementary Table S1; the total number of residues in the dataset is 13 373, out of which 1211 residues are DNA-binding (=TP+FN) and 12 162 residues are non-DNA-binding (=FP+TN).