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
Z-Score
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 http://www.bonvinlab.org/software/haddock2.2/manual/ and refer also to our online tutorials at http://www.bonvinlab.org/education
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: