Dear Amber users,
I am working with protein-ligand interaction . 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. What sort of analyses 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? Can anyone help me to proceed further with this
problem.
Few more queries in this regard are given below..
1. Does side chain dihedral angle ( Calpha-Cbeta and Cbeta-Cgamma) order
parameters can provided some information about conformational changes? If
so, does Amber (cpptarj/ptraj) have a way to calculate the same?
2. Even though there are publications, which report about the backbone
dihedral angle PCA calculations, on a similar line, is it possible to do
side-chain dihedral angle PCA? And how Amber can help me in this?
Waiting for your valuable reply.
Thanks in advance
Regards
Anu
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Received on Thu Apr 04 2013 - 05:30:02 PDT
