Prediction Of Aa Binding

Question

[royinavon]

i have two proteins with solved structure on pdb: protein A & protein B. it is known that those proteins interact in vivo. is there a server or a way to predict (or to know exactly) the binding of A to B (one sequence of aa to another)?

thank you

Answer 1

[Woa]

How about a protein-protein docking?

Answer 2

[David Westergaard]

I would be very surprised if there exists a reliable method to do this. When two proteins interact, I don't think it is unusual for some kind of conformational change to occur. Predicting a conformational change of just one protein is difficult, predicting the conformational change of two proteins simultaneously would be extremely difficult - And even if successful, the question is: how reliable is the information? What you want to do is essentially the same as virtual screening (docking), and even for small molecules, the results are very unreliable.

I think your best bet would be to dig into the articles describing the protein-protein interaction and see if they mention or suggest any modes of binding.