Table 2.
A detailed analysis of the suboptimal alignment space for selected protein pairs
| Query/target | Number of secondary structure elements | Total number of alignments | Distance to structural alignmenta |
| 1huw/1cnt1 | 4 | 1 × 106 | 4800 |
| 1yhb/1pfsA | 5 | 2 × 106 | 5 × 105 |
| 2ligA/256bA | 5 | 4 × 107 | 36 |
| 1neu/1fna | 6 | 5 × 107 | 2 × 105 |
| 1dcoA/1xxaA | 6 | 1 × 108 | 3 × 106 |
| 1urnA/1aps | 7 | 1 × 108 | 2 × 107 |
| Query/target | RMSD of the best scoring FFAS alignmentb | RMSD of the best alignment from hybrid method | RMSD of structural alignment |
| The results of direct enumeration of suboptimal alignments within reduced alignment spaces and the effectiveness of the suboptimal alignment calculations with the hybrid method. | |||
| a Distance to structural alignment is defined as the number of alignments scoring better than the structural alignment (e.g., number of alignments between the best scoring alignment and structural alignment. | |||
| b (RMSD) Root mean square deviation; (FFAS) Fold and Function Assignment System. | |||
| 1huw/1cnt1 | 15.0 | 10.5 | 2.9 |
| 1yhb/1pfsA | 9.8 | 3.3 | 3.3 |
| 2ligA/256bA | 14.3 | 6.6 | 2.9 |
| 1neu/1fna | 15.2 | 5.8 | 3.2 |
| 1dcoA/1xxaA | 12.8 | 7.1 | 2.8 |
| 1urnA/1aps | 11.5 | 7.9 | 3.2 |