Task 4 (MSUD)
Contents
Explore structural alignments
Results
Discussion
Use structural alignments to evaluate sequence alignments
Results
The following table shows an overview of the structures used for building models, the scores of the structural alignment (RMSD and LGA_S - structure similarity score), and the scores of the sequence alignment (E-value, probability and sequence identity).
| model | RMSD | LGA_S | E-value | probability | sequence identity |
|---|---|---|---|---|---|
| 1qs0 | 1.24 | 84.085 | 5.8E-94 | 100.0 | 38 |
| 1w85 | 1.77 | 78.356 | 8.3E-87 | 100.0 | 33 |
| 2ozl | 1.63 | 74.027 | 3.2E-69 | 100.0 | 27 |
| 2yic | 2.45 | 41.732 | 5.7E-47 | 100.0 | 16 |
| 3l84 | 2.01 | 32.412 | 6.5E-18 | 99.5 | 21 |
| 2q28 | 1.86 | 25.398 | 1.6E-08 | 97.9 | 13 |
| 1r9j | 1.73 | 30.095 | 1.1E-06 | 97.2 | 25 |
| 2vk8 | 2.12 | 21.990 | 3.7E-05 | 96.4 | 22 |
| 1t9b | 1.83 | 23.724 | 0.0011 | 94.9 | 18 |
| 2c31 | 2.00 | 21.849 | 0.011 | 92.7 | 21 |
| e-value | log10(e-value) | probability | sequence identity | |
|---|---|---|---|---|
| RMSD | 0.15 | 0.49 | -0.19 | -0.74 |
| LGA_S | -0.33 | -0.98 | 0.71 | 0.82 |
As can be seen in the above table, the RMSD has a weak correlation to the logarithm of E-value and a higher correlation to sequence identity. The RMSD is lower, if the E-value is lower or the sequence identity is higher.
The same tendency can be seen for the LGA_S score, but here the correlations are higher. The LGA_S score shows also a correlation to the probability in contrast to the RMSD.
The signs are opposite for RMSD and LGA_S, because the RMSD is lower for higher similarity, but the LGA_S is higher.
The relationship of LGA_S and E-value, the pair of scores with the highest correlation, for the 10 models is shown in the following plot.
