[gmx-users] Dihedral angle PCA

Thomas Evangelidis tevang3 at gmail.com
Fri Apr 12 11:28:12 CEST 2013

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

> 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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