My lab has recently screened a library of compounds. The compounds are meant to represent chemical diversity across chemical space. We would like to supplement our experiments with in silico work.
Using the pubchemy python API, I have systematically retrieved the chemical properties and SMILES for each compound in our lab screen (1600+ compounds). However, I would like to add to this by downloading additional compounds that we are yet to screen. On a drug-by-drug basis, I would usually turn to PubChem, but I'm hoping to perform some in silico analysis on large sets of compounds.
Are there any recommendations for databases of drugs/small molecules that hold chemical property and SMILES data? My preference would be a download of files rather than a web query, if possible.