Free RCSB + AlphaFold lookup · Dock tools
Search PDB by Protein Name
Find high-resolution PDB IDs from a protein name and dock in one click — or fall back to AlphaFold when no crystal exists.
Search results will appear here — ranked for molecular docking prep.
How to find a PDB ID by protein name
You do not need to memorize four-character codes or dig through the full RCSB advanced search UI. This free PDB ID finder queries the RCSB Search API in your browser, sorts by resolution, and links straight into online docking.
- 1
Type a protein name or abbreviation
Use common gene or protein names students actually search — EGFR, ACE2, HER2, CDK2, Spike protein, Mpro. Prefer the widely used abbreviation if the full systematic name returns noisy hits.
- 2
Filter by species (optional)
Default is Homo sapiens (Human). Switch to Mus musculus (Mouse) for murine coursework constructs, or All when the organism is unknown. Species filters reduce wrong-ortholog downloads before docking.
- 3
Pick a high-resolution hit and dock
Results are sorted so lower Å (better experimental detail) rises to the top. Open the RCSB page to confirm holo/apo and pocket completeness, then click Dock with this PDB to prefill AutoDock Vina on Dock.
Popular proteins students search in the PDB
Course labs and early virtual screening almost always start from a named target, not a random PDB ID. Click a protein to run a live RCSB search ranked for docking preparation.
| Protein | Typical use | Docking tip |
|---|---|---|
| Kinase / oncology coursework | Prefer kinase-domain holo entries (~≤2.5 Å) | |
| Viral entry / COVID-era labs | Check human species + ligand-bound pocket | |
| Receptor tyrosine kinase | Confirm extracellular vs kinase construct | |
| Cell-cycle docking tutorials | Many ATP-site co-crystals available | |
| SARS-CoV-2 RBD teaching sets | Filter human ACE2-complex when relevant | |
| Main protease (e.g. 6LU7 lineage) | Classic Vina homework receptor |
Why search the PDB by protein name for molecular docking?
Lab manuals and assignments name targets in English (“dock against EGFR”, “use human ACE2”), but AutoDock Vina needs a concrete receptor coordinate file — usually a four-character PDB ID from the RCSB Protein Data Bank. Students lose time browsing dozens of entries that differ by resolution, organism, domain boundaries, and whether a co-crystal ligand defines the pocket.
This free online PDB search tool is built for that long-tail workflow: you know the protein name, you need a defensible high-resolution structure, and you want to dock next — not install local scripts or memorize IDs like 6LU7. We query RCSB from the browser, prefer entries with reported resolution, sort lower Å first, and show species so you can avoid wrong-ortholog downloads.
After you pick an ID, click Dock with this PDB to open the Dock homepage with the receptor prefilled. Pair it with a ligand SMILES — convert drug names with our chemical name to SMILES converter — then run online AutoDock Vina with a downloadable report. For structure choice theory (holo vs apo, missing loops), see Does molecular docking need a crystal structure?.
PDB selection checklist for docking
Resolution alone is not enough. Before you click Dock, skim the RCSB summary with this student-friendly checklist.
- Resolution: prefer ≤ ~2.5 Å when available (lower number = finer detail).
- Organism: match the species your assignment specifies (usually human).
- Holo vs apo: prefer ligand-bound pockets for rigid-receptor Vina when possible.
- Missing residues: check that binding-site backbone is present (no giant unresolved loops).
- Chain / domain: confirm you are docking the intended kinase domain, protease, or RBD — not a wrong construct.
- Method: X-ray and competitive cryo-EM both work; NMR ensembles need extra care for coursework.
How to choose a PDB for molecular docking?
Short FAQ answers for students who searched “find PDB by protein name”, “PDB ID finder”, or “best PDB for docking EGFR / ACE2”.
Prefer a structure with the lowest numerical resolution (e.g. 1.5 Å is better than 3.0 Å) — that usually means denser experimental data and clearer side-chain density near the binding site.
When possible, pick a holo (ligand-bound) structure of the correct species, check that the pocket residues are present (no large unresolved loops), and confirm the chain you will dock against. Then click Dock with this PDB to load the ID into our online AutoDock Vina workflow.
Related docking tools
- 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.
- Lipinski Rule of 5 & Drug-likeness Checker
Paste SMILES to compute MW, LogP, HBD, and HBA with RDKit.js in-browser — pass/fail Lipinski filter before docking.
- SMILES / SDF / PDB → PDBQT Converter
Free PDB to PDBQT online (also SDF/SMILES) with Open Babel — no MGLTools. Download Vina-ready files or dock in the cloud.
- Online AutoDock Vina docking
Paste PDB ID + SMILES, review the binding box, and run docking with a downloadable report.
- Molecular docking step-by-step
Student-oriented walkthrough from structure choice to interpreting affinity scores.
- Crystal structure guide (holo vs apo)
When PDB choice matters most for rigid-receptor docking and redock checks.
- All free docking prep tools
Browse the full tools hub — PDB finder, name to SMILES, PDB cleaner, grid box, Rule of 5, PDBQT.