Extract canonical SMILES strings from SDF ligand files, one record at a time or in batch. Learn more
Extract canonical SMILES strings from SDF ligand files, one record at a time or in batch. Learn more
Extract canonical SMILES strings from SDF ligand files, one record at a time or in batch. Learn more
Convert single SMILES strings or small batches into 3D SDF files with downloadable per-entry files and a combined batch output.
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 MOL2 ligand files into SMILES strings for registration, filtering, and downstream analysis.
Convert SMILES strings into InChI strings with batch support and downloadable outputs.
Convert SMILES strings into 3D MOL2 files for docking and molecular modeling workflows.
Convert SMILES strings into 3D PDB files for molecular visualization and downstream docking preparation.
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 single SMILES strings or small batches into 3D SDF files with downloadable per-entry files and a combined batch output.
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 MOL2 ligand files into SMILES strings for registration, filtering, and downstream analysis.
Convert SMILES strings into InChI strings with batch support and downloadable outputs.
Convert SMILES strings into 3D MOL2 files for docking and molecular modeling workflows.
Convert SMILES strings into 3D PDB files for molecular visualization and downstream docking preparation.
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”.
SDF to SMILES converts SDF (Structure Data File) ligand records into SMILES strings using RDKit. SDF is the dominant 3D ligand exchange format in drug discovery — virtual screening libraries, docking outputs, and PDB ligand extractions are commonly distributed as SDF. Converting to SMILES is the standard step for registering hits in a compound database, applying 2D property filters, or feeding compounds into ML-based ADMET and toxicity predictors that require SMILES input.
ProteinIQ performs the conversion on the server through RDKit, requiring no local software installation.
Paste one or more SDF blocks directly into the text area, or upload an .sdf or .sd file. Multi-record SDF files — where individual compound records are delimited by $$$$ — are accepted and split automatically. Up to 10 entries are processed per job.
| Format | Description |
|---|---|
| Pasted SDF block | Single or multi-record SDF content pasted as text |
.sdf / .sd file | File upload; multi-record files are split automatically |
Each record produces an individual SMILES file. A combined TSV batch file is also generated, listing all successfully converted entries with their names and SMILES strings.
| File | Description |
|---|---|
Per-entry .smi | Individual SMILES string for each SDF record |
batch.tsv | Combined tab-separated file with all entries (name + SMILES) |