I am a webserver user of Haddock2.4 and I want to make a sulfated modified glycan and protein binding, but I look at the manual supported by the carbohydrate does not have a name for the sulfated group, please ask me what I should do.
thank you for your support.
If you want to dock a sulfonated carbohydrate to your protein, then define the glycan as HETATM giving it a unique residue name and unique atom names.
We followed that strategy for example to dock heparin.
This might require some manual editing of your glycan file.
Hello, I have a question, how to represent sulfonated groups in the pdb file?
HETATM 1 S SO4
HETATM 2 OS1 SO4
HETATM 3 OS2 SO4
HETATM 4 OS3 SO4
This doesn’t seem to work. I looked at the HADDOCK2.4 library and I didn’t see any way to chemically modify carbohydrates.
We do not have support for sulfonated glycans with the supported glycans listed on the website (see: https://bianca.science.uu.nl/haddock2.4/library)
One solution is to define you full glycan as HETATM. If you have multiple units, it should be defined as a single residue with non-overlapping atom names.
But this will only work if you are docking a glycan (and not dealing with a glycosylated protein as in that case the connectivity to the protein would not be created).