CAPRI Metrics - FCC Measurement

HADDOCK
1

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab

Hello,

I’m a molecular biologist and a newbie to the docking field. So if my question is irrelevant or very basic, I’d like to apologize ahead for my ignorance.

I’ve docked my complexes in HADDOCK and obtained results that are parallel with wetlab. I want to assess the quality of my models with a universal metric. I’ve seen that HADDOCK scores would give me which model is better if I compare them among each other, but because I cannot validate models I’ve generated with HADDOCK in wetlab, I need some kind of metric that would do so. I’ve seen that there’re assesment criteria provided by CAPRI. I need to measure FCC as I have three proteins docked in HADDOCK. What should I use to measure FCC?

P.S. I tried to run DockQ on my computer but I received many warning messages and I wasn’t successful.

Thank you for your concern and understanding.

2

CAPRI metrics, DockQ and FCC can only be calculated given a reference structure.

If you are trying to predict a complex, these can not be calculated (or at best with respect to the best model generated).

The selection of clusters / best models is based on the HADDOCK score.
You can not evaluate their quality with CAPRI metrics in your case.

Also if you want to compare different proteins, be aware that score is not equal to binding affinity.

3

Thank you so much professor for your swift reply.

Yes, I am trying to predict a complex. I did homology modeling by basing my prediction on PDB: 6BCU. In my case, one protein was different from the crystal structure. I cannot use 6BCU as reference, and it seems to me that I could only infer that the prediction is possible by considering negative HADDOCK and vdW, electrostatic, and desolvation energy scores. Is that so?

Thank you for your understanding and patience.