ADL: problems with Ki values, extremes Ki

Miguel Quiliano Meza qilime at yahoo.es
Fri Apr 3 22:57:34 PDT 2009


Dear Dockers.
 
I have a doubt about Ki obtained in Autodock 4. According to experimental researches, my compound shows a  Ki = 2uM, but in silico shows a Ki= 4yM (y=yocto). Somebody had the same experience..??
 
Here some details and questions:
 
* My protein was modelling by homology (identity = 44%), the active site has the same residues.
 
*In silico calculations, the analogous compounds keep the proportion of Ki, that means a>b>c in the same way that experimental Ki, but the problem as you can see are the units... uM is very different that yM.
 
* yM is the result of  a flexible docking (flexible residues 2 = active site).
 
* A rigid docking shows a Ki= 98uM (very far of 2uM, I think).
 
It is well know that try to replicate experimental Ki is very difficult in docking programs, especially with proteins obtained from homology modelling.
 
I would like to know if I could use the information of conformation (complex ligand-protein), to propose or discuss a possible mode of action of my ligand.
 
thanks in advance.
 
Miguel Quiliano


      


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