Difference between revisions of "Task 9: MSUD - Normal Mode Analysis"

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[[File:NMAmode9.gif|200px|thumb|left|Here the Mode 9 from WebNM@ is shown.]]
 
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[[File:NMAmode10.gif|200px|thumb|left|Here the Mode 10 from WebNM@ is shown.]]
[[File:Mode-7-2.gif|200px|thumb|left|These views are prepared from three orthologuous viewpoints with MolScript. Secondary structures are determined from the C-alpha atom positions of your protein (N-terminal blue, C-terminal red).]]
 
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[[File:NMAmode11.gif|200px|thumb|left|Here the Mode 11 from WebNM@ is shown.]]
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[[File:NMAmode12.gif|200px|thumb|left|Here the Mode 12 from WebNM@ is shown.]]
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Revision as of 20:52, 9 July 2012

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.

Eigenvalue plot
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

Mode 7 to 12 Atomic Displacement plots

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

Correlation matrix

The correlation matrix shows how the movements of individual atoms relates to each other. Two red collored positions correlate in their movement, blue ones anti-correlate and white redions don't correlate.

Note to myself: check if regular patterns match secondary structures.

Mode Visualization

insert flashy pictures of wiggling proteins here.

Here the Mode 7 from WebNM@ is shown.
Here the Mode 8 from WebNM@ is shown.
Here the Mode 9 from WebNM@ is shown.
Here the Mode 10 from WebNM@ is shown.
Here the Mode 11 from WebNM@ is shown.
Here the Mode 12 from WebNM@ is shown.

ElNemo

Mode 7

Here the Mode 7 from Elnemo is shown in blue, underlying in transparent green the crystal structure of bckdha_human
These views are prepared from three orthologuous viewpoints with MolScript. Secondary structures are determined from the C-alpha atom positions of your protein (N-terminal blue, C-terminal red).
These views are prepared from three orthologuous viewpoints with MolScript. Secondary structures are determined from the C-alpha atom positions of your protein (N-terminal blue, C-terminal red).
These views are prepared from three orthologuous viewpoints with MolScript. Secondary structures are determined from the C-alpha atom positions of your protein (N-terminal blue, C-terminal red).

Mode 8

Here the Mode 8 from Elnemo is shown in blue, underlying in transparent green the crystal structure of bckdha_human
These views are prepared from three orthologuous viewpoints with MolScript. Secondary structures are determined from the C-alpha atom positions of your protein (N-terminal blue, C-terminal red).
These views are prepared from three orthologuous viewpoints with MolScript. Secondary structures are determined from the C-alpha atom positions of your protein (N-terminal blue, C-terminal red).
These views are prepared from three orthologuous viewpoints with MolScript. Secondary structures are determined from the C-alpha atom positions of your protein (N-terminal blue, C-terminal red).

Mode 9

Here the Mode 9 from Elnemo is shown in blue, underlying in transparent green the crystal structure of bckdha_human
These views are prepared from three orthologuous viewpoints with MolScript. Secondary structures are determined from the C-alpha atom positions of your protein (N-terminal blue, C-terminal red).
These views are prepared from three orthologuous viewpoints with MolScript. Secondary structures are determined from the C-alpha atom positions of your protein (N-terminal blue, C-terminal red).
These views are prepared from three orthologuous viewpoints with MolScript. Secondary structures are determined from the C-alpha atom positions of your protein (N-terminal blue, C-terminal red).

Mode 10

Here the Mode 10 from Elnemo is shown in blue, underlying in transparent green the crystal structure of bckdha_human
These views are prepared from three orthologuous viewpoints with MolScript. Secondary structures are determined from the C-alpha atom positions of your protein (N-terminal blue, C-terminal red).
These views are prepared from three orthologuous viewpoints with MolScript. Secondary structures are determined from the C-alpha atom positions of your protein (N-terminal blue, C-terminal red).
These views are prepared from three orthologuous viewpoints with MolScript. Secondary structures are determined from the C-alpha atom positions of your protein (N-terminal blue, C-terminal red).

Mode 11

Here the Mode 11 from Elnemo is shown in blue, underlying in transparent green the crystal structure of bckdha_human
These views are prepared from three orthologuous viewpoints with MolScript. Secondary structures are determined from the C-alpha atom positions of your protein (N-terminal blue, C-terminal red).
These views are prepared from three orthologuous viewpoints with MolScript. Secondary structures are determined from the C-alpha atom positions of your protein (N-terminal blue, C-terminal red).
These views are prepared from three orthologuous viewpoints with MolScript. Secondary structures are determined from the C-alpha atom positions of your protein (N-terminal blue, C-terminal red).