ADL: PubChem Online Compound Search and Download

Rudy J. Richardson rjrich at
Fri May 25 16:39:34 PDT 2012

I suppose there is a difference between zero net charge on the molecule 
and no charged groups anywhere in the molecule.

On Fri, 25 May 2012, Nancy wrote:

> Hi All,
> I have been using the PubChem database to search for uncharged small
> molecules.  However, even after specifying zero charge, PubChem still
> outputs compounds containing amino groups (-NH2) and carboxylic acids
> (-COOH); since I am interested in physiological pH, these compounds would
> actually be charged.
> Is there some way to exclude molecules containing these functional groups?
> I've noticed that there is an option on PubChem to include only certain
> atoms, but the search times out at 2 minutes if I try this.  I'd like to
> exclude halogens and aldehydes as well, can this be specified?  Finally,
> after searching for numerous compounds, how could all of them be downloaded
> into an organized compound library?
> If there is another online compound database besides PubChem that can be
> easily searched and has the same or better functionality, I'd greatly
> appreciate any info about it.
> Thanks,
> Nancy
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