Free PubChem lookup · Dock tools
Instantly generate Canonical SMILES and a 2D structure from any drug, natural product, or IUPAC name — ready for molecular docking.
A free Molecular Docking tool — get a SMILES, then dock online in one click. Open docking homepage
Use English drug names or IUPAC names (e.g. Aspirin). Chinese and other non-Latin names are not supported by PubChem.
Search results will appear here — SMILES, 2D structure, and a one-click dock link.
You do not need ChemDraw, Open Babel, or a local PubChem install. This free converter calls the PubChem PUG REST API in your browser and returns a docking-ready SMILES string in seconds.
Use a common drug name (Aspirin), INN, trade name synonym, or full IUPAC name. Prefer the most widely used synonym if the first attempt fails.
We resolve the name against PubChem, show the 2D depiction, and display the Canonical (connectivity) SMILES you can copy for notebooks, scripts, or Autodock Vina input.
Click Dock with this Ligand to open our AutoDock Vina form with the SMILES prefilled. Pair it with a PDB ID (or use our protein-name PDB finder) and run docking in the browser.
Coursework and early virtual screening often start from familiar molecules. Click a name to look up the live PubChem SMILES, then dock against your target PDB.
| Compound | Typical use | Notes |
|---|---|---|
| NSAID / teaching ligand | CC(=O)Oc1ccccc1C(=O)O | |
| Drug-like carboxylic acid | CC(C)Cc1ccc(C(C)C(=O)O)cc1 | |
| Natural product flavonoid | Polyphenol scaffold (look up live) | |
| Kinase inhibitor classic | Larger oral oncology ligand | |
| Nucleotide analog | Antiviral / COVID-era example | |
| Steroid scaffold | Rigid fused-ring ligand |
Papers and lab manuals name ligands in English (“quercetin”, “remdesivir”), but docking engines need a machine-readable structure. SMILES (Simplified Molecular Input Line Entry System) encodes atoms and bonds as a single line of text — no SDF upload required for a single compound. Online AutoDock Vina pipelines typically embed that SMILES into 3D, assign protonation at a chosen pH, then write a ligand PDBQT for scoring.
Searching PubChem by name is the fastest way to get a trusted Canonical SMILES when you do not already have a ChemDraw file. This page is built for that long-tail query: you know the compound, you need the string, and you want to dock next — not install RDKit or Open Babel locally.
After conversion, pair the ligand with a receptor PDB ID. If you only know the protein name (EGFR, ACE2, CDK2), use our PDB search by protein name tool, then run docking on the Dock homepage.
Short answers for students converting drug names, IUPAC names, and synonyms into docking-ready SMILES strings.
SMILES is a compact text notation for molecular structures. Atoms and bonds are written as characters — for example aspirin is often CC(=O)Oc1ccccc1C(=O)O. Rings, branches, charges, and (in some dialects) stereochemistry all fit in one line that databases and docking tools can parse.
Find high-resolution PDB IDs from a protein name (EGFR, ACE2, HER2) and dock in one click.
Convert SMILES to SDF or MOL, or turn SDF, MOL, and PDB back into SMILES — in the browser. Look up a chemical name on the same page.
Strip HOH waters and optional HETATM records from a PDB in your browser — docking-ready receptor prep.
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.
Paste SMILES to compute MW, LogP, HBD, and HBA with RDKit.js in-browser — pass/fail Lipinski filter before docking.
Free PDB to PDBQT online (also SDF/SMILES) with Open Babel — no MGLTools. Download Vina-ready files or dock in the cloud.
Paste PDB ID + SMILES, review the binding box, and run docking with a downloadable report.
Browse the full tools hub — PDB finder, name to SMILES, PDB cleaner, grid box, Rule of 5, PDBQT.