Free in-browser conversion · Dock tools
SMILES Converter
SMILES to SDF or MOL, structure files back to SMILES, or a chemical name to a SMILES line — then dock it.
Drop a structure file
.sdf / .mol / .pdb / .smi — conversion stays in your browser
The first run downloads Open Babel once. Later conversions stay on this device.
Result
Converted files show up here. SDF and MOL also download automatically.
How to convert SMILES
SMILES is a text line for a molecule. SDF and MOL are the structure files most drawing tools and docking prep steps expect. This page converts among those formats in the browser, and can look up a chemical name on PubChem when you do not have a SMILES yet.
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Pick a direction
SMILES → SDF or MOL builds a 3D structure file (hydrogens at pH 7.4). SDF / MOL / PDB → SMILES reads a file back to a SMILES line. Chemical name → SMILES uses PubChem.
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Paste or upload
One SMILES per line is enough for a batch of small ligands. For files, drop the SDF, MOL, or PDB. Names such as Aspirin work in the name field.
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Download, or dock
Copy the SMILES into a spreadsheet, download the structure file, or send the SMILES into AutoDock Vina on Dock. PDBQT for a local Vina command line is a separate converter.
Try a molecule
These fill the form. They are not saved.
| Compound | Typical use | What you get |
|---|---|---|
| Small drug, easy first test | SMILES ↔ a compact SDF | |
| Coursework NSAID | Flexible chain, still ligand-sized | |
| Rigid heterocycle | Short SMILES, clean 3D embed | |
| Natural-product flavonoid | Common student ligand |
Which converter to use
Use this page when the search is “SMILES converter”: you have a SMILES and need SDF or MOL, or you have a structure file and need the SMILES line. Chemical name to SMILES is the same PubChem lookup, if you only need the name step.
A SMILES or SDF from here is what the Dock form accepts for AutoDock Vina. It is not a PDBQT file. Local Vina and AutoDock still want PDBQT — use the PDBQT converter for that download, or skip the file and dock online.
SMILES conversion questions
Related docking tools
- Search PDB by Protein Name
Find high-resolution PDB IDs from a protein name (EGFR, ACE2, HER2) and dock in one click.
- Chemical Name to SMILES
Convert drug or IUPAC names into Canonical SMILES via PubChem — ready for AutoDock Vina.
- PDB Cleaner — Remove Water & Heteroatoms
Strip HOH waters and optional HETATM records from a PDB in your browser — docking-ready receptor prep.
- AutoDock Vina Grid Box Calculator
Upload a reference ligand PDB/SDF to compute Center X/Y/Z and Size for your Vina search box — copy config.txt in one click.
- Dock the SMILES with AutoDock Vina
PDB ID plus this SMILES. No local Vina or Open Babel install.
- All free docking prep tools
Browse the full tools hub — PDB finder, name to SMILES, PDB cleaner, grid box, Rule of 5, PDBQT.