Table 3.
Alignment accuracy on the top 10 SP3 templates for the 1192 benchmark set.
| GDT-TS score to native‡ | ||||
|---|---|---|---|---|
| Benchmark set | CASP9 set | |||
| 874 Easy | 318 Hard | 80 Easy | 32 Hard | |
| Change relative to SP3* | Change relative to SP3 | Change relative to SP3 | Change relative to SP3 | |
| SP3 alternative alignment | 2.9% | 2.6% | 2.6% | 3.2% |
| HHSEARCH alignment | 0.7% | −2.9% | 1.4% | −2.8% |
| TM-align alignment | 15.3% | 40.7% | 16.7% | 38.8% |
| Comparison with TM-align | ||||
| Correct match# | Correct match | Correct match | Correct match | |
| SP3 alignment | 58.95/68.09/72.17 | 12.87/19.04/23.16 | 58.58/67.21/71.02 | 19.80/25.84/29.73 |
| SP3 alternative alignment | 60.77/70.62/74.47 | 13.09/19.61/23.96 | 60.19/69.08/72.75 | 20.75/27.96/32.23 |
| HHSEARCH alignment | 59.70/68.67/72.56 | 12.01/17.97/21.88 | 60.04/68.57/72.50 | 18.61/24.63/28.84 |
‡
GDT-TSscores are calculated using full length models built from alignments with MODELLER28.
*
Defined as (model GDT-TS of this method – model GDT-TS of SP3)/(model GDT-TS of SP3).
#
Correct match is defined as that when the threading and structural alignments of the target residue to the template residue are identical, within ±1, or ±2 (third number) residues apart. The number of matches in a given target is normalized by alignment length of TM-align41. Presented numbers are the average per target per template and in percentages.