Positive HADDOCK score for glycosylated protein–protein docking

HADDOCK
1

Hello,

I performed protein–protein docking using HADDOCK2.4. My system includes one glycosylated protein (prepared via CHARMM-GUI) and another non-glycosylated protein (antibody). After docking, I noticed that all top clusters have positive HADDOCK scores, even though the docking seems to converge well (binding pocket is defined in RCSB protein structures and papers).

Could the presence of glycans or their partial parameterization be responsible for these positive scores?

2

Check the components of the score to understand where the positive score comes from.

Could be your restraints.

3

The positive score was indeed caused by the restraints in the system.After reducing them, I’ve now obtained a negative score.

Thank you :slight_smile:

4

You can always refine your model using the refinement server of HADDOCK. This will remove the restraint energy terms and optimise the interface.

Or simply subtract 10% of the restraint energy from the score to get the score without the restraints contribution

5

Thank you for the suggestion, I’ll try refinement server to see differences in scores and poses.