I am using the HADDOCK docking server to perfom a protein with a dsDNA. I’m having trouble interpreting the more specific scores as the energy values. Comparing the results bellow which is in a “normal” range of scores to a protein-dna docking ?
Cluster 1 5
HADDOCK Score -128.4 +/- 11.0 -123.5 +/- 8.5
Cluster size 15 7
RMSD from the overal 25.4 +/- 0.1 22.1 +/- 0.3
lowest-energy structure
Van der Waals energy -90.9 +/- 6.5 -86.2 +/- 2.5
Electrostatic energy -430.3 +/- 29.8 -642.9 +/- 33.3
Desolvation energy -0.5 +/- 2.8 31.7 +/- 2.4
Restraints violation energy 490.6 +/- 77.52 596.2 +/- 36.48
Buried Surface Area 2255.1 +/- 140.8 2478.4 +/- 108.2
Z-Score -1.3 -0.9
I read the manual, the HADDOCK protocol described at nature journal and some articles of the group to search more details about these score values that could help with a qualitative analysis, but only deals with extracting the values. It doesn’t help me interpret a “good” score. Please, can anybody help me with this task? Thank you in advance.
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There no real saying in what is a good of bad score.
BAD for sure would be a positive score.
Also you can not compare two different systems. There is no correlation between score and binding affinity for example (we published several paper on this topic).
The question are:
- Is this cluster unique?
- if not, is it significantly better than the next cluster?
- Does it satisfy the data you have?
- Does it explain the biological knowledge you might have on the system?
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Okay… Thanks for your reply, professor!
Hi professor,
I got the Haddock score as 171, does it mean there is no interaction?
thank you
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It probably only means you have a high restraint energy. I.e. your models are not satistying the restraints you defined.
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