Question: Prediction Of Aa Binding
gravatar for royinavon
5.7 years ago by
royinavon0 wrote:

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

pdb ppi prediction • 1.7k views
ADD COMMENTlink modified 5.7 years ago by David Westergaard1.4k • written 5.7 years ago by royinavon0
gravatar for Woa
5.7 years ago by
United States
Woa2.7k wrote:

How about a protein-protein docking?

ADD COMMENTlink written 5.7 years ago by Woa2.7k
gravatar for David Westergaard
5.7 years ago by
Copenhagen, Denmark
David Westergaard1.4k wrote:

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.

ADD COMMENTlink written 5.7 years ago by David Westergaard1.4k
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