Normal mode analysis HEXA

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Revision as of 13:32, 14 July 2011 by Uskat (talk | contribs) (Results)

Webnma

General information

Results

We analysed the five models with the lowest energy values. Webnma calculates fourteen different models with following energy values:

Mode Index Deformation Energy
7 1041.88
8 1318.21
9 1738.30
10 2841.31
11 3135.09
12 4100.18
13 3911.06
14 5337.50
15 5741.69
16 6513.85
17 6081.05
18 6882.96
19 7514.14
20 7943.67

We took the first five models (7, 8, 9, 10, 11).

Here you can see the normalized squared atomic displacments of our models:

model 7 model 8 model 9 model 10 model 11
normalized squared atomic displacments of model 7
normalized squared atomic displacments of model 8
normalized squared atomic displacments of model 9
normalized squared atomic displacments of model 10
normalized squared atomic displacments of model 11


Here you can see the motion of our analyses.

model 7 model 8 model 9 model 10 model 11
normalized squared atomic displacments of model 7
normalized squared atomic displacments of model 8
normalized squared atomic displacments of model 9
normalized squared atomic displacments of model 10
normalized squared atomic displacments of model 11

Discussion

El Nemo

General information

Results

Discussion

Anisotropic Network Model web server

General information

Results

Here you can see the B-factor distribution of the real occuring B-factors (black) and the calulated B-factors (blue).

model 1 model 2 model 3 model 4 model 5
Distribution of the B-factors and the calculated B-factors in Model 1
Distribution of the B-factors and the calculated B-factors in Model 2
Distribution of the B-factors and the calculated B-factors in Model 3
Distribution of the B-factors and the calculated B-factors in Model 4
Distribution of the B-factors and the calculated B-factors in Model 5

In the next table, the motion of the protein of the different models is shown:

model 1 model 2 model 3 model 4 model 5
Calculated motion of the ANM model 1
Calculated motion of the ANM model 2
Calculated motion of the ANM model 3
Calculated motion of the ANM model 4
Calculated motion of the ANM model 5

Discussion

NOMAD-Ref

General information

Results

model 1 model 2 model 3 model 4 model 5
Histogram of the cRMS for model 1
Histogram of the cRMS for model 2
Histogram of the cRMS for model 3
Histogram of the cRMS for model 4
Histogram of the cRMS for model 5


model 1 model 2 model 3 model 4 model 5
model 1
model 2
model 3
model 4
model 5

All-atom NMA using Gromacs on the NOMAD-Ref server

General information

Results

600K

Here you can see the motion of 1BPT at temprature 600K.

model 7 model 8 model 9
normalized squared atomic displacments of model 7
normalized squared atomic displacments of model 8
normalized squared atomic displacments of model 9

2000K

Here you can see the motion of 1BPT at temprature 2000K.

model 7 model 8 model 9
normalized squared atomic displacments of model 7
normalized squared atomic displacments of model 8
normalized squared atomic displacments of model 9

Comparison to NOMAD-Ref