On 12 April 2013 07:51, anu chandra <anu80...@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 > > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
