Problem with interpretation HADDOCK scores

HADDOCK
1

Hello everyone, I am writing to you for guidance on interpreting the values I get from HADDOCK.

I am running analyzes with several sets of “ligand - receptor”, among them “positive” groups that have been confirmed with functional experiments, another group of “negatives” that have also been confirmed that they do not present an interaction in a functional way and finally a group of “artificial” that should not present interaction because they are not related and have different characteristics. My problem is that when I get the HADDOCK values, they are similar, none of them are really different.
The values that I show below were obtained by indicating the hotspots in the program.
Example:
(positive) Ligand1-Receptor1: HADDOCK score -48.3 / zcore -1.5
(negative) Ligand 2- Receptor2: HADDOCK score -63.0 / zscore -1.3
(artificial) Ligand 3- Receiver 3: HADDOCK score -39.9 / zscore -1.3

The values that I now show were obtained by default (same as above), obtaining positive values.
Example:
(positive) Ligand1-Receptor1: HADDOCK score 131.3 / zcore -1.3
(negative) Ligand 2- Receptor2: HADDOCK score 181.8 / zscore -1.5
(artificial) Ligand 3- Receiver 3: HADDOCK score 133.7 / zscore -1.9

Could you please guide me as to what is happening or what I am doing wrong? Or what values do I take as “correct”?

I thank you in advance, I remain attentive.

2

Well - the answer is simple: scores are not equal to binding affinity. And you can only compare scores of similar systems.
If your receptors are different, you can’t really compare the scores.

Further, you might want to remove the restraint energy from the score (subtract 10% of the reported restraint energy from the score).

The values that I show below were obtained by indicating the hotspots in the program.
Example:
(positive) Ligand1-Receptor1: HADDOCK score -48.3 / zcore -1.5
(negative) Ligand 2- Receptor2: HADDOCK score -63.0 / zscore -1.3
(artificial) Ligand 3- Receiver 3: HADDOCK score -39.9 / zscore -1.3

The values that I now show were obtained by default (same as above), obtaining positive values.

What do you mean by “default”? The positive scores must reflect high restraint energy.