How to Download Ligands from PubChem for Docking (SDF, SMILES, 3D)

By BioDockify Computational Research Team · September 3, 2026 · Tutorials

Download ligands from PubChem for docking correctly: 3D SDF vs SMILES, conformer availability, bulk libraries via PUG REST, and mistakes that ruin dockings.

Read the complete article with tables, code and references on BioDockify.

Key References

• Kim S et al. PubChem 2023 update. Nucleic Acids Res. 2023;51:D1373-D1380. doi:10.1093/nar/gkac956
• O\u2019Boyle NM et al. Open Babel: an open chemical toolbox. J Cheminform. 2011;3:33. doi:10.1186/1758-2946-3-33
• PubChem documentation and PUG REST API, pubchem.ncbi.nlm.nih.gov.

Scope & Limitations

PubChem conformers are computed, not experimental; docking results still depend on your sampling