Table 1.
Tests on SABmark database
| Method | SABmark-twi (209/10667) | SABmark-sup (425/19092) | ||
|---|---|---|---|---|
| Q-score | GDT-TS | Q-score | GDT-TS | |
| PROMALS3D (D + S) | 0.602 | 0.264 | 0.805 | 0.417 |
| PROMALS3D (F + S) | 0.555 | 0.220 | 0.779 | 0.390 |
| PROMALS3D (T + S) | 0.540 | 0.249 | 0.766 | 0.412 |
| PROMALS3D (D + F + S) | 0.611 | 0.256 | 0.812 | 0.414 |
| PROMALS3D (D + T + S) | 0.603 | 0.264 | 0.805 | 0.421 |
| PROMALS3D (F + T + S) | 0.595 | 0.251 | 0.800 | 0.413 |
| PROMALS3D (D + F + T + S) | 0.616 | 0.260 | 0.812 | 0.420 |
| 3DCoffee (D + S) | 0.574 | 0.252 | 0.802 | 0.421 |
| 3DCoffee (SAP + S) | 0.553 | 0.222 | 0.786 | 0.390 |
| Expresso webserver | 0.508 | 0.206 | – | – |
| PROMALS3D (D/2 + S) | 0.475 | 0.198 | 0.716 | 0.364 |
| 3DCoffee (D/2 + S) | 0.261 | 0.100 | 0.573 | 0.294 |
| 3DCoffee (D/2 + SAP) | 0.255 | 0.095 | 0.572 | 0.289 |
| PROMALS | 0.393 | 0.154 | 0.665 | 0.336 |
| SPEM | 0.326 | 0.124 | 0.628 | 0.318 |
| MUMMALS | 0.196 | 0.081 | 0.522 | 0.278 |
| ProbCons | 0.166 | 0.058 | 0.485 | 0.246 |
| MAFFT-linsi | 0.184 | 0.070 | 0.510 | 0.264 |
| MUSCLE | 0.136 | 0.056 | 0.433 | 0.233 |
| T-Coffee | 0.134 | 0.048 | 0.429 | 0.223 |
| ClustalW | 0.127 | 0.057 | 0.390 | 0.221 |
| MUSTANG | 0.550 | 0.230 | 0.779 | 0.404 |
| PROMALS3D (D) | 0.594 | 0.252 | 0.802 | 0.415 |
The first 13 methods for MSAs use both sequence and 3D structural information. The last two methods assemble multiple alignments solely from structural constraints. The other methods construct multiple alignments using only sequence information (PROMALS and SPEM also use predicted secondary structures). The letters inside the parenthesis after the method names are: ‘D’, using DaliLite structural constraints; ‘F’, using FAST structural constraints; ‘T’, using TM-align structural constraints; ‘S’, using sequence information; ‘SAP’, using SAP structural alignments; ‘D/2’, using DaliLite alignments for half of the sequences; ‘SAP/2’, using SAP alignments for half of the sequences. Q-score is the alignment quality score defined as the number of correctly aligned residue pairs divided by the total number of residue pairs in a reference alignment. GDT-TS is a reference-independent measure of alignment quality based on structural similarity of two structures superimposed according to a test alignment. The ‘twi’ stands for ‘twilight-zone’ set and ‘sup’ stands for ‘superfamilies’ set. The number of multiple alignment tests and pairwise reference alignments are shown in parentheses. The best scores are in bold letters.