Interpretation of the Haddock results HADDOCK

Is there a list where I can read a description about each result?

HADDOCK score -77.1 +/- 5.1
Cluster size 10
RMSD from the overall lowest-energy structure 4.9 +/- 0.2
Van der Waals energy -36.4 +/- 5.7
Electrostatic energy -302.1 +/- 39.9
Desolvation energy 16.9 +/- 4.0
Restraints violation energy 28.7 +/- 16.09
Buried Surface Area 1052.8 +/- 29.7

Do you mean to understand the meaning of the various terms?

I would refer to our HADDOCK web server papers (Nature Protocol 2010 and JMB 2016) and also consult the online HADDOCK manual pages at and refer also to our online tutorials at

Can I follow this thread? This link tells us the calculation for HADDOCK score

Is that correct that the displayed “HADDOCK score” in the final cluster result refers to “HADDOCKscore-water”?

For Z-Score, it indicates how many standard deviations from the average this cluster is located in terms of score (the more negative the better). I think this Z-Score only refers to the “spreading” of the structures within a cluster. Why Z-Score is used to rank the cluster?

The z-score is calculated based on the cluster averages and thus does not reflect the spread within a cluster

It is only a statistical measure of where a cluster sits with respects to the average score of all clusters

By definition the top ranked cluster will always have the most negative z-score.

Thank you. Can I ask the equation for the z-score? I found it difficult to understand how many standard deviations from the average this cluster is located in terms of score.

I can see the “HADDOCK score” is also ranked from low to high. So whether “HADDOCK score” or “z-score” is better to indicate the binding affinity?

We use the Haddock score to select clusters, but it is not a proxy for binding affinity

Thanks, so “binding affinity” is not a proper phrase to interpret the “Haddock score”. Can I ask what could be the proper physiochemical phrase to best describe “Haddock score”? e.g. binding energy? I tried to look for a suitable one through the paper and manual. It sounds like this:

The residues with lower “Haddock score” are the ones most likely to have NMR chemical shift perturbation when binding.

Is that correct?

I would not write that. The fact that residues are in contact can explain the NMR chemical shifts. But if you want more quantitative analysis check:

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