Nomenclature of Glycans

HADDOCK
1

Hello all, I want to analyse glycosaminoglycan docking, for which I was trying to change the nomenclature of glucose rings according to the HADDOCK library supported carbohydrates. One of the monosaccharide units of Heparin are in L conformation and none of the supported structures in HADDOCK are in L conformation. So which nomenclature should be used for the glucose ring with L conformation?

Thanks in advance for your help.

2

We don’t have any support for heparin building blocks I am afraid.

If not too long (<10 units) you can try to define it as one residue, with unique atom names for all units and as HETATM