Task 9: Normal Mode Analysis

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Revision as of 15:02, 9 August 2011 by Meier (talk | contribs) (Webnma)

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

Der server WEBnm@ uses only the C-alpha atoms to calculate the normal modes.

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

ElNemo

Anisotropic Network Model web server

oGNM – Gaussian network model

NOMAD-Ref

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