Question: Get SMILES strings from all compounds with bioactivity data in PubChem
0
gravatar for miquelduranfrigola
5.3 years ago by
Barcelona
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?

Thanks!

pubchem • 3.7k views
ADD COMMENTlink modified 5.3 years ago by David Westergaard1.4k • written 5.3 years ago by miquelduranfrigola760
1
gravatar for David Westergaard
5.3 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 (ftp://ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/) and join it with the structural data (ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/). However, an alternative solution might also be to use the ChEMBL database (https://www.ebi.ac.uk/chembldb/). They integrate a lot of the PubChem bioassay data, as well as data from the literature and provide several ways of accessing it (http://chembl.blogspot.co.uk/2014/06/mychembl-launchpadlaunched.html)

 

Hope that helped!

ADD COMMENTlink written 5.3 years ago by David Westergaard1.4k
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