On 15/04/2020 22:07, Green, Todd Jason wrote:
I have a peptide with an O-linked disaccharide that I would like to
model and/or dock to a protein binding partner. I can generate the
glycopeptide. So, I wanted to first try and manually dock it to the
protein. For the manual docking, I was wondering if there is a tool
for coot or another graphics program to apply a series of preferred
conformation to the glycans (in relation to the protein side chain to
which it is linked), somewhat like you would do for a side chain
rotamer. This is pure ab initio modeling, ie. not into electron
density. Anyone have a suggestion?
The tools in Coot for O-linked carbohydrate are not implemented as they
are for N-linked carbohydrate. Not today at least. So what you want to
do is not easy in Coot.
Maybe Glycan Builder can help:
http://glycan-builder.cermav.cnrs.fr/
Once you have your initial model, there are several O-linked links in
the dictionary, FUC-THR, NAG-THR, MAN-THR, NAG-SER so they should just
work. Then you can use multi-residue torsion. JED-Flip and
regularization - but there is nothing carbohydrate-specific about that.
Paul.
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