Interface energy vs binding energy

Member Site Forums Rosetta 3 Rosetta 3 – General Interface energy vs binding energy

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    • #1821

        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?


      • #9768

          If you’re looking at protein-protein binding, I would highly recommend using the InterfaceAnalyzer to do your post analysis. 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.)

        • #9770

            Thank you very much for your sugestion, rmoretti.

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