[Chimera-users] PubChem Online Compound Search and Download

Nancy nancy5villa at gmail.com
Fri May 25 15:52:58 PDT 2012

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.

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