Convert SMILES strings into 3D MOL2 files for docking and molecular modeling workflows.
Convert InChI strings into SMILES with batch support and downloadable outputs.
Convert MDL MOL ligand files into canonical SMILES strings for registration, filtering, and downstream analysis.
Convert SDF ligand files, including multi-record batches, into SMILES strings.
Convert SMILES strings into InChI strings with batch support and downloadable outputs.
Convert SMILES strings into 3D PDB files for molecular visualization and downstream docking preparation.
Convert single SMILES strings or small batches into 3D SDF files with downloadable per-entry files and a combined batch output.
Run Open Babel in the browser to convert chemical and structure files, with coordinate, hydrogen, and pH options where the WASM runtime supports them.
Convert Protein Data Bank files to Structure Data Format
Convert Structure Data Format files to Protein Data Bank format
Convert SMILES strings into 3D MOL2 files for docking and molecular modeling workflows.
Convert InChI strings into SMILES with batch support and downloadable outputs.
Convert MDL MOL ligand files into canonical SMILES strings for registration, filtering, and downstream analysis.
Convert SDF ligand files, including multi-record batches, into SMILES strings.
Convert SMILES strings into InChI strings with batch support and downloadable outputs.
Convert SMILES strings into 3D PDB files for molecular visualization and downstream docking preparation.
Convert single SMILES strings or small batches into 3D SDF files with downloadable per-entry files and a combined batch output.
Run Open Babel in the browser to convert chemical and structure files, with coordinate, hydrogen, and pH options where the WASM runtime supports them.
Convert Protein Data Bank files to Structure Data Format
Convert Structure Data Format files to Protein Data Bank format
Configure inputs to begin
Set options on the left, then click “Submit job”.
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.
ProteinIQ handles the conversion through RDKit on the server, so no local installation of any cheminformatics toolkit is required.
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 |
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 |