Question: Protein Interface Comparison
0
gravatar for Reyhaneh
6.2 years ago by
Reyhaneh480
United Kingdom
Reyhaneh480 wrote:

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 ;

interaction comparison protein • 1.2k views
ADD COMMENTlink modified 6.2 years ago by João Rodrigues2.5k • written 6.2 years ago by Reyhaneh480
1
gravatar for Woa
6.2 years ago by
Woa2.7k
United States
Woa2.7k wrote:

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

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Woa2.7k
0
gravatar for João Rodrigues
6.2 years ago by
João Rodrigues2.5k
Stanford University, U
João Rodrigues2.5k wrote:

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?

ADD COMMENTlink written 6.2 years ago by João Rodrigues2.5k
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