Table 1.
Assessing the effectiveness of 3 distance measures (FASTA, STRUCTAL on 3D sequence traces, and STRUCTAL on 3D structures) in identifying proteins with similar structures.
| MDS spacea |
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| FASTA |
3DSEQ |
3DSTRUCT |
||||||||||
| Cluster | 2 | 3 | 4 | 5 | 2 | 3 | 4 | 5 | 2 | 3 | 4 | 5 |
| 1 | 30.8b | 36.6 | 43.6 | 47.6 | 34.5 | 41.7 | 47.0 | 50.6 | 39.7 | 60.7 | 62.2 | 77.0 |
| 2 | 32.6 | 38.9 | 45.2 | 49.5 | 31.3 | 39.7 | 46.0 | 50.2 | 56.8 | 71.0 | 72.2 | 76.6 |
| 3 | 27.7 | 34.4 | 41.4 | 45.5 | 44.1 | 50.9 | 56.7 | 59.4 | 82.5 | 87.1 | 88.00 | 90.9 |
| 4 | 28.3 | 34.9 | 42.4 | 47.3 | 31.8 | 40.0 | 45.5 | 49.3 | 40.7 | 54.5 | 56.9 | 71.2 |
| 5 | 28.7 | 35.0 | 41.3 | 45.6 | 33.2 | 42.2 | 49.3 | 52.9 | 50.2 | 67.0 | 70.4 | 74.6 |
| AIS | 29.6c | 35.9 | 42.8 | 47.1 | 35.0 | 42.9 | 48.9 | 52.5 | 54.0 | 68.0 | 70.0 | 78.1 |
a
Dimension P of the MDS projected space, i.e. number of coordinates representing each protein. Fig. 7 provides illustrations of this space for P = 2.
b
Average distance dav = 0.25 ∑ j ≠ id(Ci, Ci), where d is computed using Eq. (10). The distances are scaled as fraction of the maximum distance between any two proteins in CATH605.
c
Average Inter-cluster Separation (AIS) computed using Eq. (10). A large value for AIS indicates a good separation between the clusters.