Hello,
Is there a (preferably free) way to download all molecules (SMILES or SDF) from a published scientific article?
Like searching pubchem or chembl or ZINC via DOI or so?
I would like to extract molecules from some papers, but I would like
to avoid having to input each molecule by hand...
Thanks a lot,
F.
I guess you can do it with SciIFinder.
https://www.lanl.gov/library/find/articles/scifinder.php
You can do this in ChEMBL using the recent web interface.
On a document report card, scroll down until "Compound summary", then click on "Associated compounds for document blablaba". It opens a page with all the compounds. Click on SDF (button upper right) and it will download a sdf file with all the compounds.
Or if you have the document chembl_id, you can just use this url: https://www.ebi.ac.uk/chembl/g/#browse/compounds/filter/_metadata.related_documents.all_chembl_ids%3ACHEMBL3621072
To do this in a more programmatic way, I would recommend to install the ChEMBL database locally. A simple SQL query will be able to return all the compound structures associated to a DOI.
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