Protein Interface Comparison

Question

[Reyhaneh]

I have two proteins which their interfaces are predicted using an interface predictor. Now I would like to compare the 2 binding sites only knowing which residues are the interfaces. The comparison i would like to do is both structural and physico-chemical properties.

Do you have any suggestion of a good tool or a good publication on this subject?

Thanks ;

Answer 1

[Woa]

Check publications from Ruth Nussinov and Ozlem Keskin

and this reference can be of some help:

http://www.future-science.com/doi/abs/10.4155/fmc.12.147

Answer 2

[João Rodrigues]

I'd rely on you. Open them in Pymol/VMD/Chimera and see what they are. Are they solvent accessible, are they clustered together, are they conserved residues, are they charged/hydrophobic, etc..

You can also just try docking them and seeing if the results make sense by then comparing interfaces (and not just predicted patches). Which predictors did you use?