Glycans
Best practice guide
HADDOCK also supports the docking of several carbohydrates. A list of glycan residues supported by HADDOCK can be found here. This page consists of the following chapters:
Tutorials
- HADDOCK3 protein-glycan modeling and docking: This tutorial shows how to use HADDOCK3 to dock a glycan to a protein, provided that some information exists about the protein binding site.
Publications
- A. Ranaudo, M. Giulini, A. Pelissou Ayuso and A.M.J.J. Bonvin. Modelling Protein-Glycan Interactions with HADDOCK. J. Chem. Inf. Mod. 64, 7816–7825 (2024).
Optimal settings for docking of glycans
| Parameter | Module / parameter | default value | optimal value |
|---|---|---|---|
| Clustering method | | ||
Cutoff for clustering in [clustrmsd] | clust_cutoff | 7.5 | 2.5 |
More about optimal settings for different docking scenarios can be found here.
FAQ
Any more questions about glycan docking with HADDOCK? Have a look at: