Difference between revisions of "Normal Mode Analysis (PKU)"
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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 [http://apps.cbu.uib.no/webnma/home webnm@] and [http://www.igs.cnrs-mrs.fr/elnemo/start.html elNemo] webservers. See the [[Task_9_-_Normal_Mode_Analysis|task description]] for details, a journal of commands and scripts, if necessary, can be found [[Task_9_-_Journal_(PKU)|here]]. |
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 [http://apps.cbu.uib.no/webnma/home webnm@] and [http://www.igs.cnrs-mrs.fr/elnemo/start.html elNemo] webservers. See the [[Task_9_-_Normal_Mode_Analysis|task description]] for details, a journal of commands and scripts, if necessary, can be found [[Task_9_-_Journal_(PKU)|here]]. |
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| + | ===Normal Mode Analysis=== |
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| + | In normal mode analysis (NMA) the protein is modeled as harmonically oscillating system to e.g. describe conformational changes. Normal modes are much faster to calculate than a molecular dynamics simulation, especially as usually few low-frequency modes suffice to describe a proteins motions.<ref name=ElNemo>Karsten Suhre and Yves-Henri Sanejouand; ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Research Volume 32, Issue suppl 2</ref> |
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== WEBnm@ == |
== WEBnm@ == |
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Revision as of 20:26, 7 July 2012
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.
Normal Mode Analysis
In normal mode analysis (NMA) the protein is modeled as harmonically oscillating system to e.g. describe conformational changes. Normal modes are much faster to calculate than a molecular dynamics simulation, especially as usually few low-frequency modes suffice to describe a proteins motions.<ref name=ElNemo>Karsten Suhre and Yves-Henri Sanejouand; ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Research Volume 32, Issue suppl 2</ref>
WEBnm@
<figure id="fig:mode7">
</figure> <figure id="fig:mode8">
</figure> <figure id="fig:mode9">
</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.
