Interface energy vs binding energy

[Anonymous]

Hi all,

I know, there is a little bit difference between interface energy and binding energy in protein docking.
Interface energy come from, separate 2 chain (same pose) far away and then calculate total energy
Interface energy= (complex total energy) – (separated total energy)

Binding energy com from , calculate total score for each individual chain (different pose)
Binding energy = (complex total energy) – [ (individual chain 1 total energy) + (individual chain 2 total energy) ]

right ?

I would like to know, which energy is suitable to compare the binding affinity between 2 different protein to a target protein in protein docking?

Thanks,

[Anonymous]

If you’re looking at protein-protein binding, I would highly recommend using the InterfaceAnalyzer to do your post analysis. https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/dc/d92/_interface_analyzer.html It outputs a large number of metrics which are useful in analyzing protein-protein interfaces.

Towards your question, it outputs a dG_separated value which is the value after physically separating and optionally repacking the two proteins. It would be this metric which I would recommend using for comparing binding energies of different complexes. (Along with the other metrics that get produced.)

[Anonymous]

Thank you very much for your sugestion, rmoretti.

[Author]

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