Normal Mode Analysis BCKDHA

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Revision as of 13:25, 14 July 2011 by Demel (talk | contribs) (NOMAD-Ref)



Anisotropic Network Model web server

oGNM – Gaussian network model


The NOMAD <ref>[[1]]</ref> server does provide a lot of information. The following parameters can be set:

Number of modes to calculate
Distance weight parameter
Cutoff to use for mode calculation
Average Rmsd in output trajectories
Method to use
    • Automatic
    • Full matrix solver
    • Sparse matrix solver
Here we used the default option, the automatic mode.

What information do the different servers provide? Which regions of your protein are most flexible, most stable? When you visualize the modes (provided by server or using for example PyMol or VMD), try to describe what movements you observe? Hinge-movement, “breathing”…

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

In order to do the all-atom NMA we needed to prepare our PDB file. The PDB file for 1BPT protein contains 1629 atoms in total, all lines not beginning with "ATOM" were removed from the PDB file.

Advantages and Disadvantages from NMA and MD


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go back to Task 8: Molecular Dynamics Simulations