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

From Bioinformatikpedia
(Anisotropic Network Model web server)
(Webnma)
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== Webnma ==
 
== Webnma ==
Der server [http://apps.cbu.uib.no/webnma/home WEBnm@] uses only the C-alpha atoms to calculate the normal modes.
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The server [http://apps.cbu.uib.no/webnma/home WEBnm@] uses only the C-alpha atoms to calculate the normal modes.
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The calculations are performed using the [http://dirac.cnrs-orleans.fr/plone Molecular Modelling Toolkit] with the C-alpha force field.
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The used input format is very easy (see below).
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[[File:PAH_WEbnma_input_field.png]]
   
 
=== Results ===
 
=== Results ===

Revision as of 17:48, 9 August 2011

There are several forces acting within a protein. Most of these forces have one or more equilibrium states. In reality the protein is flexible. That means, that the atoms of the system swing around these equilibrium states. These swinging around the equilibrium states can be approximated by the harmonic approximation. The forces can then be replaced by a less complex system of springs. With this model it is possible to calculate large motions of the protein by Normal Mode Analysis.

In opposite to Molecular Dynamics this is very fast and it is not a simulation it is a calculation of possible simple and large motions.

In this task we want to try several servers, which calculate normal mode analysis. A detailed description of the task can be found here. For most runs we used the structure 1J8U for our protein PAH. In the case of the all-atom NMA we used a smaller protein to test the server and this kind of approach.

Webnma

The server WEBnm@ uses only the C-alpha atoms to calculate the normal modes. The calculations are performed using the Molecular Modelling Toolkit with the C-alpha force field.

The used input format is very easy (see below).

PAH WEbnma input field.png

Results

Plots of atomic displacement

Mode 7

PAH WEBNMA Mode7plot.png

Mode 8

PAH WEBNMA Mode8plot.png

Mode 9

PAH WEBNMA Mode9plot.png

Mode 10

PAH WEBNMA Mode10plot.png

Mode 11

PAH WEBNMA Mode11plot.png

Visualization of Normal Modes

Mode 7

PAH webnma Mode7.gif

Mode 8

PAH webnma Mode8.gif

Mode 9

PAH webnma Mode9.gif

Mode 10

PAH webnma Mode10.gif

Mode 11

PAH webnma Mode11.gif

ElNemo

Results

Low Collectivity of Mode 4:

PAH ELNEMO COLLECTIVITY.png

Visualization of Normal Modes

Mode 7

PAH ELNEMO Mode7 1.gif PAH ELNEMO Mode7 2.gif PAH ELNEMO Mode7 3.gif

Mode 8

PAH ELNEMO Mode8 1.gif PAH ELNEMO Mode8 2.gif PAH ELNEMO Mode8 3.gif

Mode 9

PAH ELNEMO Mode9 1.gif PAH ELNEMO Mode9 2.gif PAH ELNEMO Mode9 3.gif

Mode 10

PAH ELNEMO Mode10 1.gif PAH ELNEMO Mode10 2.gif PAH ELNEMO Mode10 3.gif

Mode 11

PAH ELNEMO Mode11 1.gif PAH ELNEMO Mode11 2.gif PAH ELNEMO Mode11 3.gif

Anisotropic Network Model web server

Results

Visualization of Normal Modes

Mode 1

PAH ANMA Mode1.gif

Mode 2

PAH ANMA Mode2.gif

Mode 3

PAH ANMA Mode3.gif

Mode 4

PAH ANMA Mode4.gif

Mode 5

PAH ANMA Mode5.gif

oGNM – Gaussian network model

NOMAD-Ref

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