Table 2. Statistics of 24 SCOP folds common to both DNA-binding and non-DNA-binding proteins in the benchmark sets.
| All | Threading | Final | |||||
| SCOP ID | Ndom | Npro | Ndom | Npro | Ndom | Npro | SCOP Fold Description |
| 46688 | 49/11 | 39/8 | 41/3 | 36/2 | 37/0 | 32/0 | DNA/RNA-binding 3-helical bundle |
| 52979 | 14/4 | 14/3 | 6/0 | 6/0 | 5/0 | 5/0 | Restriction endonuclease-like |
| 49379 | 7/26 | 7/23 | 1/0 | 1/0 | 1/0 | 1/0 | Diphtheria toxin/TFs/cytochrome f |
| 47768 | 7/1 | 6/1 | 6/0 | 5/0 | 4/0 | 3/0 | SAM domain-like |
| 47458 | 5/1 | 5/1 | 5/0 | 5/0 | 5/0 | 5/0 | HLH-like |
| 57943 | 5/44 | 5/44 | 5/15 | 5/15 | 5/3 | 5/3 | Parallel coiled-coil |
| 53334 | 4/19 | 4/19 | 4/9 | 4/9 | 1/1 | 1/1 | SAM-dependent methyltransferases |
| 53066 | 4/34 | 4/20 | 1/0 | 1/0 | 0/0 | 0/0 | Ribonuclease H-like |
| 54861 | 3/98 | 3/95 | 0/3 | 0/3 | 0/0 | 0/0 | Ferredoxin-like |
| 55603 | 6/1 | 3/1 | 6/0 | 3/0 | 1/0 | 1/0 | Homing endonuclease-like |
| 100938 | 2/1 | 2/1 | 2/0 | 2/0 | 2/0 | 2/0 | SPOC domain-like |
| 47953 | 4/10 | 2/6 | 4/8 | 2/4 | 4/4 | 2/2 | Cyclin-like |
| 56218 | 2/2 | 2/2 | 2/2 | 2/2 | 1/0 | 1/0 | DNase I-like |
| 57715 | 2/11 | 2/5 | 0/0 | 0/0 | 0/0 | 0/0 | Glucocorticoid receptor-like |
| 46954 | 2/2 | 2/1 | 2/0 | 2/0 | 0/0 | 0/0 | Putative DNA-binding domain |
| 81302 | 1/8 | 1/8 | 0/1 | 0/1 | 0/0 | 0/0 | Nucleotidyltransferase |
| 55944 | 2/13 | 1/13 | 0/4 | 0/4 | 0/2 | 0/2 | TBP-like |
| 55810 | 1/12 | 1/11 | 0/12 | 0/11 | 0/0 | 0/0 | Nudix |
| 50485 | 1/2 | 1/2 | 1/0 | 1/0 | 0/0 | 0/0 | FMT C-term domain-like |
| 46556 | 1/10 | 1/10 | 0/0 | 0/0 | 0/0 | 0/0 | Long α-hairpin |
| 53755 | 1/6 | 1/6 | 0/3 | 0/3 | 0/0 | 0/0 | UDP-Glycosyltransferase/glycogen phosphorylase |
| 51350 | 1/218 | 1/216 | 0/4 | 0/4 | 0/0 | 0/0 | TIM α/β-barrel |
| 50352 | 1/30 | 1/23 | 0/0 | 0/0 | 0/0 | 0/0 | β-Trefoil |
| 52539 | 2/82 | 1/80 | 0/0 | 0/0 | 0/0 | 0/0 | P-loop containing nucleoside triphosphate hydrolases |
| Total | 127/646 | 109/599 | 86/64 | 75/58 | 66/10 | 58/8 | |
Ndom and Npro denote the numbers of domains and proteins from DB179/NB3797, respectively. The statistics were collected for all targets, targets detected by threading (Z-score>6), and the final positives after applying the energy filter. These three sets of numbers are indicated by All, Threading, and Final, respectively.