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

[vivek modi]

Thanks a lot Tsjerk.
I really appreciate the help.



Regards,
-Vivek.




> Message: 6
> Date: Tue, 1 Nov 2011 17:35:54 +0100
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] PCA on secondary structure of protein.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <CABzE1SisyAAwP1Wx43bygbQcfR5Wa47mto13VZHGd+sD7mr13g at mail.gmail.com
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> Sure!
>
> 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.
>
> :)
>
> Tsjerk
>
> 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
> > IITK.
> >
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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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