Request for Guidance on Analyzing Protein-Protein Docking Results

HADDOCK
1

Dear HADDOCK Team,

I hope this message finds you well.

I have performed docking simulations between proteins A and B, as well as between proteins A and C using the HADDOCK tool. From these simulations, I have obtained the following scoring metrics:

HADDOCK score
Cluster size
RMSD from the overall lowest-energy structure
Van der Waals energy
Electrostatic energy
Desolvation energy
Restraints violation energy
Buried Surface Area
Z-Score
However, I am uncertain about how to comprehensively analyze these metrics to determine whether the docking between A and B is better or worse compared to the docking between A and C. Therefore, I am seeking your expertise on how to scientifically and effectively compare these docking results based on the provided scoring metrics.

Thank you very much for your assistance.

Best regards,

2

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3

Hi,

The HADDOCK score should not be used to compare different complexes, but rather to inspect the results obtained within each run. Similar systems might be compared, but I don’t know how similar proteins B and C are in your case.

Have a look at this other thread Problem with interpretation HADDOCK scores

PS: I notice you have a very high restraint energy, maybe check your restraints and/or remove the 10% of that value from the overall HADDOCK score

Cheers

4

Thank you :coffee:

5

I have connected A-B(TLR2) and A-C(TLR4). However, I can only perform kinetic simulations on one of these complexes, and I am struggling to find a reason to choose between them. Do you have any suggestions?

Thank you.

6

May-be some MD simulations first could help. Check for example:

Not really meant to compare different complexes though but rather different clusters of the same complex.

7

If I am docking the same 2 proteins with different ligands, can I compare between them?

8

That would be a better case indeed for comparison.
But again, remember that the score is not equal to binding affinity.