[gmx-users] Dihedral angle PCA

[Mark Abraham]

On Fri, Apr 12, 2013 at 11:28 AM, Thomas Evangelidis <tevang3 at gmail.com>wrote:

> On 12 April 2013 07:51, anu chandra <anu80125 at gmail.com> wrote:
>
> > Hi David,
> >
> > Thanks for the reply. I have not tried yet. Since I didn’t find query
> about
> > the dihedral PCA in the mail list, I thought of confirm about the steps
> > mentioned in the web site.
> >
> >
> > Regarding the use of dihedral PCA, the protein with which I am working
> > behave differently from others. From literature, this protein shows
> minimal
> > backbone conformational changes during ligand binding and presumed that
> > there is high degree of side-chain conformational changes during binding
> to
> > ligand. This made me to think about dihedral PCA for get some information
> > about the ligand binding. What is your opinion in this regard?
> >
> >
> Why not Cartesian PCA restricted to the protein backbone ?


Ja. Fit to the backbone, and measure on the side chains. In principle, any
kind of difference metric could work. RMSD of side chain atoms vs backbone
atoms is all you need for "are the side chains the ones changing upon
binding?"


> dPCA is
> preferred in cases of peptides or intrinsically disordered proteins.
>

And even then a disordered mess can still be a disordered mess...

Mark


> > Is there any other sort of analyses that can help me to quantify such
> > side-chain conformational changes and also to locate the regions in
> > protein, which have  high degree of side-chain conformational changes
> > during ligand binding?
> >
> > Waiting for your valuable reply.
> >
> > Thanks and regards
> > Anu
> >
> >
> >
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