Question: Get SMILES strings from all compounds with bioactivity data in PubChem
gravatar for miquelduranfrigola
6.1 years ago by
miquelduranfrigola760 wrote:

Hi all,

I need the full list of CIDs (and corresponding SMILES string) of compounds that have been screened in BioActivity assays in PubChem.

What is the easiest way to obtain it?


pubchem • 4.4k views
ADD COMMENTlink modified 6.1 years ago by David Westergaard1.4k • written 6.1 years ago by miquelduranfrigola760
gravatar for David Westergaard
6.1 years ago by
Copenhagen, Denmark
David Westergaard1.4k wrote:

Though I have not dealt with the same problem, the easiest way is probably to download the data directly from their FTP site ( and join it with the structural data ( However, an alternative solution might also be to use the ChEMBL database ( They integrate a lot of the PubChem bioassay data, as well as data from the literature and provide several ways of accessing it (


Hope that helped!

ADD COMMENTlink written 6.1 years ago by David Westergaard1.4k
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