Table 1.
Comparison of structural alignments obtained with MAMMOTH and with other methods
| Protein 1 | Protein 2 | MAMMOTH | SHEBA | OTHERS |
| 1acx | 1cob_B | 77 | 69 | 90 (1) |
| 1acx | 1tmf−A | 25 | — | 80 (1) |
| 1pts_A | 1mup | 75 | 72 | 76 (1) |
| 2gbl | 1ubq | 45 | 44 | 42 (2) |
| 2gb1 | 4fxc | 42 | 44 | 39 (2) |
| 1ubq | 4fxc | 60 | 54 | 48 (2) |
| 1plc | 2rhe | 64 | 49 | 50 (2) |
| 1plc | 1acx | 51 | 57 | 48 (2) |
| 1acx | 1rbe | 62 | 59 | 49 (2) |
| 1aba | 1trs | 65 | 64 | 60 (3) |
| 1aba | 1dsb_A | 36 | 52 | 47 (3) |
| 1aba | 1pbf | 47 | 51 | 36 (4) |
| 1mjc | 5tss_A | 42 | 54 | 50 (4) |
| 1pgb | 5tss_A | 45 | 43 | 43 (4) |
| 2tmv_P | 256b_A | 68 | 68 | 64 (4) |
| 1tnf_A | 1bmv_I | 54 | 80 | 71 (4) |
| 1ubq | 1frd | 60 | 56 | 48 (4) |
| 2rsl_C | 3chy | 55 | 59 | 56 (4) |
| 3chy | 1rcf | 99 | 89 | 75 (4) |
This set is taken from Jung and Lee. Table 2 (Jung & Lee, 2000). For each pair, the number of aligned residues after optimal structural alignment, as obtained with the different programs, is shown.
(1) Dali (Holm & Sander, 1993); (2) MLC (Boutonnet et al., 1995); (3) VAST (Madej et al., 1995; Gibrat et al., 1996); (4) ProSup (Lackner et al., 2000)