Table 1. Summary of template identification by different alignment methods.
| TM-scoreb | RMSD (Å)c | Coveraged | |||||
|---|---|---|---|---|---|---|---|
| Methodsa | First | Best in top10 | First | Best in top10 | First | Best in top10 | CPUe |
| Profile-to-profile alignments | |||||||
| MUSTER | 0.435(0.449) | 0.487(0.512) | 10.3(15.2) | 8.7(12.3) | 0.875 | 0.875 | 27.0 |
| HHsearch-II | 0.429(0.449) | 0.477(0.507) | 9.5(21.6) | 9.0(14.1) | 0.767 | 0.820 | 13.0 |
| dPPAS | 0.426(0.438) | 0.481(0.502) | 9.6(20.6) | 8.5(15.3) | 0.819 | 0.844 | 17.0 |
| PPAS | 0.424(0.441) | 0.473(0.499) | 10.3(17.4) | 8.9(13.4) | 0.839 | 0.850 | 10.0 |
| SP3 | 0.424(0.438) | 0.476(0.499) | 10.7(15.7) | 9.1(12.3) | 0.873 | 0.873 | 11.0 |
| HHsearch-I | 0.422(0.444) | 0.472(0.502) | 9.5(20.3) | 9.0(14.7) | 0.763 | 0.817 | 16.0 |
| SPARKS | 0.421(0.433) | 0.469(0.493) | 11.0(15.7) | 9.4(12.1) | 0.891 | 0.886 | 36.0 |
| PROSPECT | 0.418(0.428) | 0.469(0.490) | 11.5(13.3) | 9.9(11.3) | 0.914 | 0.903 | 15.0 |
| PPA | 0.397(0.413) | 0.447(0.469) | 10.9(17.5) | 9.7(15.5) | 0.844 | 0.851 | 25.0 |
| FFAS | 0.393(0.406) | 0.444(0.465) | 9.5(24.2) | 8.6(18.9) | 0.758 | 0.790 | 4.0 |
| PRC | 0.372(0.388) | 0.417(0.442) | 8.6(32.9) | 8.0(24.3) | 0.668 | 0.712 | 23.0 |
| Average | 0.415(0.429) | 0.465(0.5) | 10.2(19.5) | 9.0(17.7) | 0.818 | 0.838 | 17.9 |
| Sequence-to-profile alignments | |||||||
| SAM | 0.344(0.358) | 0.405(0.426) | 10.6(27.5) | 9.9(18.3) | 0.717 | 0.778 | 8.0 |
| PSA | 0.338(0.333) | 0.371(0.392) | 12.9(17.5) | 12.0(15.0) | 0.870 | 0.873 | 9.0 |
| PSI-BLAST | 0.301(0.320) | 0.344(0.369) | 7.8(51.7) | 7.4(42.1) | 0.507 | 0.556 | 4.0 |
| Average | 0.328(0.337) | 0.373(0.4) | 10.5(32.3) | 9.8(25.1) | 0.698 | 0.736 | 7.0 |
| Sequence-to-sequence alignments | |||||||
| NW-align | 0.321(0.336) | 0.377(0.403) | 12.7(21.7) | 11.4(15.0) | 0.849 | 0.866 | 5.0 |
| SW-align | 0.265(0.285) | 0.324(0.348) | 9.9(49.5) | 9.2(35.7) | 0.560 | 0.625 | 4.0 |
| BLAST | 0.246(0.263) | 0.292(0.315) | 8.5(59.7) | 8.2(47.5) | 0.470 | 0.529 | 0.1 |
| Average | 0.277(0.295) | 0.331(0.424) | 10.4(43.7) | 9.7(23.6) | 0.626 | 0.673 | 3.0 |
| Other controls | |||||||
| TM-align | 0.661(0.664) | 0.663(0.683) | 3.1(7.5) | 3.0(7.1) | 0.856 | 0.846 | 90.0 |
| MUSTERSS + BTA + SA | 0.482(0.511) | 0.512(0.559) | 8.0(14.1) | 7.2(11.2) | 0.797 | 0.800 | 26.0 |
| MUSTERSS + BTA | 0.453(0.481) | 0.493(0.536) | 9.5(12.7) | 8.1(11.3) | 0.831 | 0.820 | 26.0 |
| MUSTERSS | 0.447(0.474) | 0.487(0.528) | 9.7(12.7) | 8.3(11.3) | 0.839 | 0.830 | 26.0 |
aAlignment methods as sorted by TM-score in each category.
bAverage TM-score. Values in parentheses are for full-length models built by MODELLER. ‘First’ refers to the top-ranking model based on alignment score; ‘Best in top10’ to the best model of the highest TM-score among the top ten models with the highest alignment scores.
cRMSD to the native.
dAlignment coverage equals to the number of aligned residues divided by target length.
eAverage CPU time in minutes, which consists of constructing profile and building of alignments in a HP DL1000h computer.