Table III.
Speedup of MASTER obtained by limiting the number of matches to the top 1000 and setting a loose initial RMSD cutoff of 2.0 Å
| Matches | Segments | ||||
|---|---|---|---|---|---|
| 1 | 2 | 3 | 4 | 5 | |
| 103−104 | 1.0–1.0 (8) | 1.0–1.6 (5) | 1.0–1.3 (6) | 1.0–1.5 (4) | 1.0–1.6 (6) |
| 104−105 | 1.0–1.1 (3) | 1.2–2.9 (4) | 1.4–4.0 (6) | 1.7 (1) | 2.3 (1) |
| 105−106 | 1.2–1.5 (4) | 1.8–7.3 (6) | 7.0–10 (3) | 5.4 (1) | (0) |
| 106−107 | 1.7–1.7 (2) | 9.6–9.6 (2) | 22 (1) | (0) | (0) |
Speedups are measured relative to searches with the same cutoff but without limiting the number of matches. Results are categorized according to the number of query segments and total number of matches under 2.0 Å. Queries for which there were fewer than 1000 matches under 2.0 Å were discarded for this analysis. Ranges of speedups in each category are indicated, with the number of examples shown in parentheses.