Normal Mode Analysis (PKU)

Short Task Description

This week, we will perform a normal mode analysis of our wildtype protein. We will calculate visualize large coordinate movements to identify e.g. domains and try to watch ligand interaction. For this, we will use the webnm@ and elNemo webservers. See the task description for details, a journal of commands and scripts, if necessary, can be found here.

WEBnm@

<figure id="fig:mode7">

Animation of mode 7 from WEBnm@. Original pdb-structure is colored green. BH4 is colored yellow and the Fe2+ ion is colored in red. The mesh represents the model gained from WEBnm@.

</figure> <figure id="fig:mode8">

Animation of mode 8 from WEBnm@. Original pdb-structure is colored green. BH4 is colored yellow and the Fe2+ ion is colored in red. The mesh represents the model gained from WEBnm@.

</figure> <figure id="fig:mode9">

Animation of mode 9 from WEBnm@. Original pdb-structure is colored green. BH4 is colored yellow and the Fe2+ ion is colored in red. The mesh represents the model gained from WEBnm@.

</figure>

elNemo

ElNemo computes ten perturbed models for the first five non-trivial normal modes of the input protein as a standard and perturbations for the lowest 25 modes on request in a separate queue. There is no fixed limit to the size or number of modes but too long running jobs will eventually be killed. The calculation uses a cutoff value to determine which atom-atom interactions are kept in the elastic network model and another parameter to determine how many residues are treated as rigid body to speed up calculation appropriately.