Get SMILES strings from all compounds with bioactivity data in PubChem

Question

[miquelduranfrigola]

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?

Thanks!

Answer 1

[David Westergaard]

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!