Residue-residue contact vs protein-protein interactions
Hi everyone, I’m concern about the problem of predicting binary protein-protein interaction. Two proteins are defined to interact if they form a complex executing a function transiently and stably, e.g. a protein-ligand binds to a protein-receptor, homo-oligomers protein. But I notice that given two imaginary protein sequences folding in the imaginary space will result in two imaginary protein structures. I use the word ‘imaginary‘ here for my thought experiment. Two structures would fluctuate dynamically and atomically, some atoms would attract others, some would repel. And expand to amino acid molecules in protein structures, some amino acids would attract other amino acids, some would repel. These two structures will have some complementary domains, some attracted domains, some repel domains. So can we from residue-residue contact (in this case is the distances in space between amino acids – contact map) to say this protein interacts with this protein or not (from my first definition).
Thank you for any of your contributions and arguments.
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