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

[vivek modi]

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
IITK.
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