Molecular Docking Server

Ligand to protein binding comparison
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Author:  PREACT_Docking1 [ Wed Aug 29, 2012 7:35 am ]
Post subject:  Ligand to protein binding comparison

Hello everyone,

How can I compare the binding / Inhibition of one ligand docked to several proteins (in different runs)? Is it valid to compare the Kd's from Ligand vs Protein, normalized to the Kd's of the endogenous subtrate to the enzyme?
Does anyone have an idea?

Thank you for your help,
Best, Robert

Author:  hazaie [ Wed Aug 29, 2012 1:35 pm ]
Post subject:  Re: Ligand to protein binding comparison

Hi Robert,

I think the first thing to compare is the "specificity" of docking.That means how many different results you got for the same docking. A good result is if there are only 1 or 2 dominant hits with high frequence and lowest energy. If you filtered your results based on this than you can compare the energy of the others.


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