Task 9: MSUD - Normal Mode Analysis
WEBnm@
WEBnm@ provides users with a number of different for Normal Mode Analysis of their protein of interest.
Deformation Energies
The deformation energies are energies associated with each node and are inversly related to the amplitude of the protein motion and thereby gives a general idea which motion is the strongest. The eigenvalues plot serves the same purpose.
| Mode Index | Deformation Energy | Mode Index | Deformation Energy |
|---|---|---|---|
| 7 | 288.99 | 14 | 2957.24 |
| 8 | 407.20 | 15 | 2715.91 |
| 9 | 589.17 | 16 | 3291.75 |
| 10 | 752.78 | 17 | 3543.09 |
| 11 | 842.47 | 18 | 3927.68 |
| 12 | 994.58 | 19 | 4115.63 |
| 13 | 1727.81 | 20 | 4950.67 |
Atomic Displacement
The atomic displacement plots show what regions in the protein move the most for the specific mode. Here regions where peaks are clustered are are of paticular interest, as single peaks only represent local flexibility. The largest observation that can be made is that for each mode largest movment happens either at the start or end of the protein (or both). This higher amounts of movement near the ends of a protein are to be expected, but as the results are normalized over the complete protein movement and the movement for the ends is so much larger than the rest we find it difficult to differentiate whether the peaks near the end are actually moving parts of the protein, or just the ends "flopping" around. For further discussion of these results please see the Mode visualition section.
Correlation Matrix
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ElNemo
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