Restraining glycans in a glycosylated protein docking using HADDOCK (locally)

HADDOCK
1

Hi all,
I want to use HADDOCK for docking a glycosylated protein with an antibody. For this purpose, I need to put some restraints to the sugar moieties (glycans). Can I get some help for the same?

Thanks!

2

In principle HADDOCK should recognise glycans.
At least the supported ones. Check for the list and naming:

https://rascar.science.uu.nl/haddock2.4/library

So if your glycans are in that list, there should be no need to define additional restraints.

3

Many thanks for your response!
I re-named the glycan residues however when I run it on the sever, the “NAG” (a supported glycan resname) units still somehow seem to be broken.
On a separate note, we would still need to define these restraints when running locally, right?

4

How many NAG do you have then?

Which units do you expect to be connected?

5

I have a fully glycosylated protein with 84 glycans attached to the ASN residues. However, not all the NAG units are falling apart.

6

in your config file you define three PDBs, so do I understand correctly that you also have glycans on the protein itself and those are the problem?

And are you trying to dock NAG and GLC onto that glycosylated protein? This is what your workflow defines.

Make sure all glycans on the protein are HADDOCK compatible / supported

7

Sorry for the confusion.
My receptor is a fully glycosylated protein (protein + gylcans) and I am trying to dock an antibody to this glycosylated protein. Glycans are just a part of protein1. I checked the list of compatible glycans and changed the names accordingly and it works fine with the updated resnames. However, I am still facing issues with the “NAG”
glycans, they are compatible with haddock but still falling apart. And surprisingly not all NAGs are falling apart but only a few (6 units). Please suggest. I have attached my umabig.tbl
comb_restraints.tbl (4.1 KB)
(where I put restrained on the NAGs that were falling apart)
file for your reference.

Thanks you!

8

but why do you then input NAG as a separate molecule? In that way you are effectively docking them.

Share may-be also your input pdb