Browser-only receptor prep · Dock tools
Strip crystallographic waters and optional heteroatoms from a PDB in your browser — then dock on Dock.
Drop a .pdb file here
or click to browse · parsing stays local · never sent to our servers
Upload a PDB above. Counts of removed waters and heteroatoms will appear here.
You do not need PyMOL scripts, Open Babel one-liners, or a local Autodock prep install just to strip crystallographic water. This free PDB cleaner parses the file with the browser FileReader API, removes HOH (and optional HETATM) records, and lets you download or dock in one click — nothing is uploaded during cleaning.
Drag and drop or browse for a Protein Data Bank file (.pdb / .ent) from RCSB, AlphaFold, or a course handout. Parsing stays on your device; we never send the file to a cleaning API.
Waters (residue names HOH, WAT, DOD, H2O) are always removed. Keep the checkbox on to also drop other heteroatoms — co-crystallized ligands, ions, and solvents. Turn it off if you need a cofactor or ion left in the pocket.
Download *_clean.pdb for local Vina/PyMOL, or click Dock with this Clean PDB to preload the cleaned receptor into our online AutoDock Vina form — still only in this browser tab until you submit a job.
Student docking tutorials usually ask you to “delete waters and heteroatoms” before converting to PDBQT. Here is exactly what the online cleaner does to each record type.
| Record / content | Default action | Why it matters for Vina |
|---|---|---|
| HOH / WAT waters | Always removed | Crystallographic waters fill the pocket and can block your ligand pose. |
| Other HETATM (ligands, ions) | Removed if checkbox on | Co-crystal ligands compete with your SMILES; ions may still be useful — choose deliberately. |
| ATOM (protein / nucleic acid) | Kept | Standard amino-acid / nucleotide coordinates stay as the receptor scaffold. |
| HEADER, TITLE, REMARK, TER, END… | Kept | Metadata and chain terminators are preserved for readability in PyMOL. |
| ANISOU / CONECT for deleted atoms | Not rewritten | Simple line filter for coursework speed; re-clean in PyMOL if you need perfect CONECT graphs. |
Almost every RCSB crystal structure ships with crystallographic waters (residue name HOH) and often a co-crystallized ligand written as HETATM records. AutoDock Vina treats those atoms as part of the rigid receptor unless you strip them first. Leaving hundreds of waters in the binding site can sterically block poses, inflate clash scores, and make student redock benchmarks look worse than the published co-crystal.
Classic desktop prep uses PyMOL (“remove resn HOH”), ChimeraX, or a shell pipeline with grep / Open Babel. That works — but it is slow when you only need a clean receptor for a homework docking run. This free online PDB cleaner is built for that long-tail workflow: download a PDB (or fetch one via our PDB search by protein name), strip HOH and optional HETATM in the browser, then dock with a ligand SMILES from our chemical name to SMILES converter.
After cleaning, click Dock with this Clean PDB to open the Dock homepage with the receptor preloaded as an upload. Online Dock still adds hydrogens and prepares PDBQT for Vina. For the full receptor/ligand checklist, see preparing receptors and ligands for AutoDock Vina and the student walkthrough how to do molecular docking step by step.
Removing waters is necessary but not sufficient. Skim this checklist after you download the clean PDB — especially for graded coursework and redock validation.
In the PDB format, most waters are stored as HETATM lines whose residue name is HOH (columns 18–20). That means “delete all HETATM” also deletes waters — but “delete only HOH” leaves ions, glycerol, PEG, and co-crystal drugs in place. This tool always strips water residue names, and optionally strips every remaining HETATM line so you can match the two common lab instructions:
Protein and DNA/RNA backbone stay as ATOM records. We do not rename chains, renumber residues, or add hydrogens here — that is intentional so the cleaner stays a transparent, auditable first step before docking.
Short answers for students searching “remove water from PDB”, “delete HETATM online”, “clean PDB for docking”, or “strip HOH before AutoDock Vina”.
No. Cleaning uses the browser FileReader API only. Coordinates stay on your machine during this step. If you later click Dock with this Clean PDB and submit a docking job, Dock receives the cleaned text you chose to run — the same as uploading a file on the homepage.
Find high-resolution PDB IDs from a protein name (EGFR, ACE2, HER2) and dock in one click.
Convert drug or IUPAC names into Canonical SMILES via PubChem — ready for AutoDock Vina.
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.
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.
Upload a cleaned receptor or paste a PDB ID, add SMILES, review the binding box, and run docking with a downloadable report.
Full prep checklist after you strip waters — protonation, PDBQT, and ligand options.
Student-oriented walkthrough from structure choice to interpreting affinity scores.
Browse the full tools hub — PDB finder, name to SMILES, PDB cleaner, grid box, Rule of 5, PDBQT.