ADL: MW bias

Douglas Houston dhouston at
Tue Apr 14 10:14:56 PDT 2009


Does this mean that I need to come up with an Autodock-specific way of  
normalizing the rankings? If flexible ligands are already penalized  
then a simple N^(1/3) will either over-penalize flexible ligands or  
under-penalize rigid ones.


Quoting Mark Swingle <mswingle at>:

> Doug,
> I would say the answer is yes. This is probably ameliorated somewhat by the
> torsional free energy penalty. OTOH, this would not help much with molecules
> that are both large and rigid.
> ISTM, that this could be corrected for after screening by normalizing the
> score to the number of heavy atoms (see e.g.   J Chem Inf Comput Sci 43
> (2003), pp. 267–272, where normalizing to N^(1/3) is recommended).
> Alternatively, a much more complex correction scheme is detailed in J Med
> Chem 47 (2004), pp. 80–89.
> Regards,
> Mark
> On Monday 09 March 2009 01:57:23 pm Douglas Houston wrote:
>> Hi all,
>> I have a general question about Autodock. Quite often docking programs
>> are biased towards ligands that are large simply because the larger a
>> molecule is the more van der Waal interactions it can make with the
>> receptor. Is Autodock affected by this bias or does its algorithms
>> include some means of compensating?
>> Thanks a lot,
>> Doug
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Dr. Douglas R. Houston
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