Task 9: MSUD - Normal Mode Analysis
From Bioinformatikpedia
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.
[[File:1U5B.pdb.mode7to12plot.png|thumb|Mode 7 Atomic Displacement plot]
ElNemo
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