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What is SDF to SMILES?
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.
How to use SDF to SMILES online
ProteinIQ performs the conversion on the server through RDKit, requiring no local software installation.
Input
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 |
Output
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) |