[gmx-users] PCA on secondary structure of protein.

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Nov 1 17:35:54 CET 2011


You'll just be looking at correlations between secondary structure
elements, disregarding the role that the loops may play. But it's a
sound approach.



On Tue, Nov 1, 2011 at 3:44 PM, vivek modi <modi.vivek2009 at gmail.com> wrote:
> Hi,
> I plan to perform PCA on a globular protein which I am studying. The
> simulation for the same is done for 100ns.
> I have small doubt. Is it appropriate to perform PCA to study the movement
> in protein on only secondary structure elements (helices in this case).
> My protein contains long loops which do not play any role. Is it appropriate
> to group only the helices together ignoring the loops and perform PCA ?
> Any help is appreciated.
> Regards,
> -Vivek Modi
> Graduate Student
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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