[Zinc-fans] vendor library filtering

John J. Irwin jji at cgl.ucsf.edu
Mon May 25 10:54:37 PDT 2009


Hi Jack

Jack Flanagan wrote:
>
> Hi all,
>
>  
>
> Firstly, this is a tremendous resource, thank you to the creators.
>
>  
>
> Secondly, I was wondering if the vendor libraries are filtered in any
> way, eg MW . That is the “usual” ones found at the bottom of the
> vendor pages.
>
>  
>
For most vendors, we filter out compounds that in our view are poor
candidates for docking.  Since ZINC is a general purpose database, our
rules are more generous than most investigators we know.  The basic
rules are here: http://filtering.docking.org/rules_default.txt
<http://blaster.docking.org/filtering/rules_default.txt>

We also have two sets of "yuck" rules to tag compounds that many people
prefer not to consider. You can find the yuck and yuck1 rules here:
http://filtering.docking.org/
<http://blaster.docking.org/filtering/rules_default.txt>   These are the
rules we use for the "clean" subsets in ZINC.

We do still load molecules that don't pass the default rules when it
suits us, e.g. the molecule is a drug, metabolite, natural product, or
patented compound.  Since the molecule is bioactive, this seems sensible
to us.

Many investigators prefer to use "clean" subsets, because it is thought
that this will reduce the number of false positives, which can be
terribly time consuming.  This does come at the price of sacrificing
some molecules, and the choice of clean or regular should probably be
made on a case by case basis. (See Babaoglu, Shoichet, et al JMC 2008)

John
UCSF ZINC Team

<http://blaster.docking.org/filtering/rules_default.txt>
>
> Thanks in advance
>
>  
>
> Jack
>
> ------------------------------------------------------------------------
>
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>   
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