Table III.
Ranking of structural alignment methods for the subset of α-helical membrane proteins
| Score | Type | FR-TM-align | TM-align | FATCAT rigid | FATCAT | Matt | LovoAlign | SKA | DaliLite | SABERTOOTH | SHEBA | CE | SAP | PPM | MAMMOTH |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CADa | Rmean | 1 | 4 | 3 | 2 | 5 | 8 | 10 | 9 | 7 | 6 | 11 | 12 | 13 | 14 |
| Rreliability | 1 | 2 | 4 | 3 | 8 | 5 | 7 | 6 | 11 | 10 | 12 | 9 | 13 | 14 | |
| mean (%) | 63.3 | 63.3 | 63.3 | 63.3 | 63.3 | 62.8 | 62.4 | 62.7 | 62.8 | 62.9 | 62.3 | 62.0 | 60.7 | 59.7 | |
| stdev (%) | 0.08 | 0.08 | 0.08 | 0.08 | 0.09 | 0.09 | 0.09 | 0.09 | 0.09 | 0.09 | 0.09 | 0.10 | 0.09 | 0.09 | |
|
| |||||||||||||||
| AL4 | Rmean | 2 | 1 | 3 | 6 | 4 | 9 | 5 | 11 | 7 | 10 | 8 | 14 | 12 | 13 |
| Rreliability | 1 | 2 | 4 | 6 | 7 | 5 | 3 | 8 | 10 | 11 | 9 | 12 | 14 | 13 | |
| mean (%) | 94.8 | 94.8 | 94.5 | 93.9 | 94.2 | 93.1 | 94.2 | 92.8 | 93.6 | 92.9 | 93.4 | 90.0 | 90.9 | 90.4 | |
| stdev (%) | 7.0 | 6.9 | 7.2 | 9.3 | 8.1 | 12.9 | 8.3 | 11.2 | 8.3 | 9.2 | 8.3 | 17.0 | 10.9 | 14.7 | |
|
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| GDT | Rmean | 1 | 2 | 3 | 5 | 4 | 9 | 10 | 8 | 6 | 7 | 11 | 12 | 13 | 14 |
| Rreliability | 1 | 2 | 7 | 8 | 6 | 3 | 4 | 5 | 10 | 11 | 9 | 12 | 13 | 14 | |
| mean (%) | 71.1 | 71.0 | 70.6 | 70.1 | 70.4 | 69.5 | 69.7 | 69.7 | 70.0 | 69.6 | 69.4 | 67.2 | 66.2 | 63.3 | |
| stdev (%) | 14.8 | 14.8 | 14.8 | 16.0 | 15.8 | 17.9 | 16.1 | 16.5 | 15.6 | 15.8 | 15.9 | 19.6 | 16.7 | 18.4 | |
|
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| aveb | Rmean | 1.3 | 2.3 | 3.0 | 4.3 | 4.3 | 8.7 | 8.3 | 9.3 | 6.7 | 7.7 | 10.0 | 12.7 | 12.7 | 13.7 |
| Rreliability | 1.0 | 2.0 | 5.0 | 5.7 | 7.0 | 4.3 | 4.7 | 6.3 | 10.3 | 10.7 | 10.0 | 11.0 | 13.3 | 13.7 | |
The structural alignment methods are sorted according to the sum of their average Rmean and Rreliability rankings, with the most accurate alignments on the left side of the table. The mean and standard deviation (stdev) of each score over all pairs of alignments are given.
a
CAD score multiplied by 100.
b
Mean ranking over all three scores. Entries in bold indicate the highest or best scores in that column and those that are not significantly different from the highest/best score, according to the Wilcoxon signed rank test, with p < 0.05.