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 ;
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written
by
Reyhaneh
2 answers
Check publications from Ruth Nussinov and Ozlem Keskin
and this reference can be of some help:
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?
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