Normal mode analysis HEXA

Webnma

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

Anisotropic Network Model web server

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

NOMAD-Ref

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

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