I want to get all Pubchem Chemical compounds (CID) that interact with a given UniProt target. I have a list of UniProt targets and I need to study the relationship between these targets and chemical compounds.
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The easiest solution to the problem of mapping chemical compounds to protein IDs is to use the ChEMBL compound ID to UniProt mapping.
Doing this with PubChem is not so straight forward in part because its downloadable data format is a hideous obfuscated and badly documented mess split over multiple compressed files which in turn contain multiple compressed files...... For a publicly funded project they should really do better.