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What is MOL2 to SMILES?
MOL2 to SMILES converts Tripos MOL2 molecular structure files into SMILES strings using RDKit. MOL2 is a 3D format common in molecular docking and scoring pipelines — carrying Tripos atom types, partial charges, and coordinates — while SMILES is the compact, connectivity-only representation preferred for database registration, compound filtering, and machine learning workflows. Converting MOL2 → SMILES is a routine step when extracting ligand identities from docking output files or from crystallographic databases that distribute structures in MOL2 format.
How to use MOL2 to SMILES online
ProteinIQ handles the conversion through RDKit on the server, so no local installation of any cheminformatics toolkit is required.
Input
MOL2 content can be pasted directly into the text area as one or more MOL2 blocks, or uploaded as a .mol2 file. Up to 10 entries are accepted per job; each entry appears as a separate molecule card.
| Format | Details |
|---|---|
| Pasted MOL2 block | One or more @<TRIPOS>MOLECULE blocks pasted into the input area |
| File upload | .mol2 file containing one or more molecule records |
Output
Each entry produces an individual SMILES file. A combined TSV batch file is also generated containing the conversion report for all entries — including molecule name, canonical SMILES, and per-entry conversion status.
| File | Contents |
|---|---|
Per-entry .smi | Canonical SMILES for the converted molecule |
batch.tsv | All entries with name, SMILES, and conversion status |