Table 2.
Comparison of top L/5 long-range contacts predicted by our three methods, MULTICOM-NOVEL, MULTICOM-CONSTRUCT, and MULTICOM-CLUSTER for the 38 free-modeling structural domains using precision measure. L, Ntarget, and Meffdomain stand for the length of the target sequence, number of sequence in the alignment for the whole target sequence, and the number of effective sequences in the alignment when alignments are trimmed to match the residues of the native structural domain, respectively. The last three columns show the precision of top L/5 long-range contacts for the three methods. The ‘Alignment’ column shows the method and parameter used to generate the alignment, where ‘jhm’ stands for JackHMMER and ‘hhb’ stands for HHblits.
| Target | FM Domain | L | Alignment | Ntarget | Meffdomain | CONSTRUCT | CLUSTER | NOVEL |
|---|---|---|---|---|---|---|---|---|
| T0859 | T0859-D1 | 133 | jhm-e-0 | 2 | 1 | 4.4 | 4.4 | 0.0 |
| T0862 | T0862-D1 | 239 | jhm-e-0 | 163 | 31 | 26.3 | 26.3 | 21.1 |
| T0863 | T0863-D1 | 670 | jhm-e-0 | 453 | 73 | 2.6 | 2.6 | 5.1 |
| T0863 | T0863-D2 | 670 | jhm-e-0 | 453 | 54 | 4.2 | 4.2 | 4.2 |
| T0864 | T0864-D1 | 246 | jhm-e-0 | 526 | 134 | 64.0 | 64.0 | 32.0 |
| T0866 | T0866-D1 | 183 | hhb-cov75 | 1388 | 560 | 100.0 | 100.0 | 14.3 |
| T0869 | T0869-D1 | 120 | jhm-e-0 | 17 | 12 | 42.9 | 52.4 | 47.6 |
| T0870 | T0870-D1 | 138 | jhm-e-0 | 137 | 81 | 16.0 | 16.0 | 40.0 |
| T0878 | T0878-D1 | 358 | jhm-e-0 | 856 | 250 | 42.0 | 42.0 | 26.1 |
| T0880 | T0880-D2 | 193 | jhm-e-0 | 2 | 1 | 25.0 | 21.9 | 18.8 |
| T0886 | T0886-D1 | 346 | jhm-1e-40 | 3013 | 1182 | 78.6 | 78.6 | 7.1 |
| T0886 | T0886-D2 | 346 | jhm-1e-40 | 3013 | 1837 | 88.5 | 88.5 | 23.1 |
| T0888 | T0888-D1 | 121 | jhm-e-0 | 2 | 1 | 8.0 | 0.0 | 0.0 |
| T0890 | T0890-D2 | 191 | jhm-e-0 | 70 | 17 | 13.6 | 13.6 | 9.1 |
| T0892 | T0892-D2 | 193 | jhm-e-0 | 579 | 202 | 54.6 | 54.6 | 63.6 |
| T0894 | T0894-D1 | 324 | jhm-e-0 | 438 | 61 | 11.1 | 11.1 | 55.6 |
| T0896 | T0896-D3 | 486 | jhm-e-0 | 2295 | 7 | 12.1 | 12.1 | 9.1 |
| T0897 | T0897-D1 | 285 | jhm-e-0 | 130 | 10 | 7.1 | 7.1 | 17.9 |
| T0897 | T0897-D2 | 285 | jhm-e-0 | 130 | 57 | 52.0 | 52.0 | 20.0 |
| T0898 | T0898-D1 | 169 | jhm-1e-4 | 50000 | 389 | 4.6 | 4.6 | 13.6 |
| T0899 | T0899-D1 | 423 | jhm-1e-10 | 6580 | 125 | 71.2 | 71.2 | 40.4 |
| T0899 | T0899-D2 | 423 | jhm-1e-10 | 6580 | 31 | 44.4 | 44.4 | 33.3 |
| T0900 | T0900-D1 | 106 | jhm-e-0 | 16243 | 1331 | 95.2 | 95.2 | 71.4 |
| T0901 | T0901-D2 | 328 | hhb-cov50 | 5167 | 127 | 64.3 | 64.3 | 42.9 |
| T0904 | T0904-D1 | 341 | jhm-1e-10 | 23741 | 609 | 72.6 | 72.6 | 29.4 |
| T0905 | T0905-D1 | 353 | jhm-1e-10 | 8623 | 346 | 79.6 | 79.6 | 63.3 |
| T0905 | T0905-D2 | 353 | jhm-1e-10 | 8623 | 88 | 42.9 | 42.9 | 42.9 |
| T0907 | T0907-D3 | 315 | jhm-e-0 | 219 | 1 | 79.2 | 79.2 | 41.7 |
| T0912 | T0912-D3 | 624 | jhm-1e-20 | 7240 | 426 | 42.9 | 42.9 | 4.8 |
| T0914 | T0914-D1 | 337 | jhm-e-0 | 325 | 70 | 6.3 | 6.3 | 31.3 |
| T0914 | T0914-D2 | 337 | jhm-e-0 | 325 | 33 | 6.1 | 6.1 | 15.2 |
| T0915 | T0915-D1 | 161 | jhm-e-0 | 34 | 21 | 48.4 | 45.2 | 29.0 |
| T0918 | T0918-D1 | 546 | jhm-1e-20 | 3517 | 356 | 77.3 | 77.3 | 40.9 |
| T0918 | T0918-D2 | 546 | jhm-1e-20 | 3517 | 487 | 88.0 | 88.0 | 20.0 |
| T0918 | T0918-D3 | 546 | jhm-1e-20 | 3517 | 513 | 66.7 | 66.7 | 0.0 |
| T0923 | T0923-D1 | 409 | jhm-e-0 | 10 | 7 | 12.1 | 19.0 | 22.4 |
| T0941 | T0941-D1 | 470 | jhm-e-0 | 3 | 1 | 2.9 | 2.9 | 1.5 |
| T0946 | T0946-D1 | 292 | hhb-cov50 | 3170 | 80 | 25.0 | 25.0 | 6.3 |
|
| ||||||||
| Average | 253 | 41.6 | 41.7 | 25.4 | ||||