Is possible to computationally determine inhibitor of protein-protein interaction?

Question

[john_well]

Hello,

I encounter such question: there are several small molecules, and people in laboratory A have tested them in protein A, and they are Active inhibiting Protein A, at the same time, people in laboratory B (they do not know people in lab A) have also tested them in Protein B, they are also Active inhibiting Protein B. In addition, it is known that protein A and protein B interact each other (directly and indirectly).

My question is: can I get the conclusion: these small molecules possibly interact with the surface of protein A and protein B complex?

Can you give some clues according to given conditions？

Thanks

[cyril-cros]

Are you considering the underlying regulatory gene network, or are you talking about purely physical interaction between your proteins? In the first case you could try to establish if your small molecules act on some regulatory genes influencing both A and B. In the second case you may consider structural modelling (which is tricky).

[john_well]

Thanks cyril-cros. In fact, I do not know if protein A and protein B have physical interaction or not. If they physical interact each other, docking between small molecules and protein-complex (or each of proteins) is needed to determine the mode of interaction between them. Right?

[alolex]

Is this a homework question? It kind of sounds like one.