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CHEMBL is public database of measured bioactivities located at the EBI, Hinxton/Cambridge.
Data retrieval can be done via the python API as described in the CHEMBL-og blog.
Please refer to a github CHEMBL project to retrieve bioactivities from the EBI/CHEMBL database.

 python retrieve-compounds.py -h
usage: backup_retrievals.py [-h] [–uniprot_id UNIPROT_ID]
[–n_struct_pic N_STRUCT_PIC] [–drugs DRUGS]
[–target_confidence TARGET_CONFIDENCE]

The script is was tested on the 5th of February 2018 using:

  • python 3.6.0.final.0
  • installed by conda 4.3.27
  • rdkit 2017.03.2
  • pycharm community edition 2017.3.3