Hello! I did two different analysis in haddock easy and used the same peptide and protein in both.
The only thing that I changed is the active residues, in one I put much less residues than the other.
In the left side is the results for the docking with less active residues in the interface, and in the right side is the docking with much more active residues in the interface.
I am a little confused about the results, and I cant decide which one is the better.
Do you have any idea?
Thank you!
It is hard to deduct anything from only one cluster for each run. Distribution of the runs and their energetics are important to draw conclusion. We often advise to look at the first 3 to 5 clusters to have a proper idea of the quality of a docking run.
Your HADDOCK scores, at least for the 1st cluster of each run, are within the standard deviation of each other, so nothing much to deduct from that. However, the size of the best cluster in your run on the left is significantly bigger than the one of the right, reporting, if the clustering parameters are the same, a better convergence there. Once again, we should have a look at the other clusters, could be that the size of the 2nd best cluster of your right run is also important and its energy within the standard deviation of the 1st cluster.
Having a look at the structure themselves is a must-do. You know your system, you might already know what to expect or not and what is biologically relevant. Looking at numbers is not enough to draw conclusions. So would be nice to compare the best models of the top3 clusters of your 2 runs for instance.
So without more information we cannot tell you what is the best, and actually even with them we would need to know a bit more of the background to emit an hypothesis.
With the runs details we could discuss further if you need more insights!
Good luck,
Mikael
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