I see binding site and interface used almost interchangeably in the literature, but I'm not sure if it is exactly the same thing or not - what is the difference?

  • $\begingroup$ By PPI do you mean protein-protein interactions? I see binding site more in the context of transcription factor binding sites (i.e. protein-DNA interactions; I may be biased here by my own experience though). It would help if you quote examples from the literature. $\endgroup$
    – ddiez
    Commented May 28, 2015 at 14:31
  • 1
    $\begingroup$ We can't give you an answer without more context. Neither of those terms is really standard, so what they mean will depend on context. Could you give some examples? $\endgroup$
    – terdon
    Commented May 28, 2015 at 15:05

1 Answer 1


A protein-protein interaction (PPI) binding site is a type of interface. If it has been established that the interface is a PPI binding site, then the terms can from that point forward be used interchangeably. But the word "interface" is very generic and does not have any specific scientific meaning so the nature of the interface must be defined or else the term is fairly meaningless.


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