Where to Get SMILES Strings

Option 1: 

PubChem 

1. Search for your compound at PubChem

2. Scroll to the "Names and Identifiers" section

3. Click "Canonical SMILES" or "Isomeric SMILES" 

Canonical SMILES → standardized form (structure only) 

Isomeric SMILES → includes stereochemistry.

Option 2: 

ChEMBL 

1. Visit ChEMBL

2. Search by name or structure.

3. Copy the canonical SMILES from the compound record.

Figure 2: Canonical smiles generation from ChEMBL

Best Practices

• Verify SMILES with a visualization tool before use

• Use isomeric SMILES when stereochemistry matters

• Keep a table with:

  • Compound name

  • CID/ChEMBL ID

  • Canonical SMILES

  • Isomeric SMILES

• Avoid copy-paste errors — check for missing atoms or misplaced numbers.

SMILES is a fundamental tool in modern chemistry. By understanding its simple rules, you can efficiently handle, store, and share molecular information for computational analysis. Whether you're building a ligand library or just cataloging compounds, mastering SMILES is a key step. Happy modeling! ✨

REFERENCES

Bento, A. P., Gaulton, A., Hersey, A., Bellis, L. J., Chambers, J., Davies, M., Krüger, F. A., Light, Y., Mak, L., McGlinchey, S., Nowotka, M., Papadatos, G., Santos, R., & Overington, J. P. (2013). The ChEMBL bioactivity database: an update. Nucleic Acids Research, 42(D1), D1083–D1090. https://doi.org/10.1093/nar/gkt1031.  

Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., & Bolton, E. E. (2020). PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Research, 49(D1), D1388–D1395. https://doi.org/10.1093/nar/gkaa971. 

PubChem: National Center for Biotechnology Information (NCBI). Retrieved from pubchem.ncbi.nlm.nih.gov.

SMILES Tutorial (EPA) – https://archive.epa.gov/med/med_archive_03/web/html/smiles.html 

Weininger, D. (1988). SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. Journal of Chemical Information and Computer Sciences, 28(1), 31–36. https://doi.org/10.1021/ci00057a005.

Wikipedia: SMILES – https://en.wikipedia.org/wiki/Simplified_Molecular_Input_Line_Entry_System