AlphaFold Structure Viewer — Open PDB & mmCIF Files, View Predictions
Open a .pdb or .cif file — every chain's sequence, missing residues, ligands and pLDDT — or look up a UniProt accession's AlphaFold prediction in 3D.
Open a PDB or mmCIF file — an RCSB entry, or a model from AlphaFold Server or ColabFold — and see what is in it under the 3D view: each chain's sequence (downloadable as FASTA), which residues have no coordinates, bound ligands, mass, pI and ε280, and the model's own pLDDT where the file carries one. The file is read in your browser, not uploaded. Or look up a protein's AlphaFold Protein Structure Database prediction by UniProt accession and explore it in an interactive 3D viewer, powered by Mol* — the same viewer used by the PDB and AlphaFold DB websites. The structure loads with AlphaFold's standard per-residue confidence (pLDDT) coloring applied automatically, and you can add one or more residue ranges — a domain, a mutation, a binding site — each highlighted in its own color directly on the 3D structure, using the same 1-based inclusive {start, end} convention as the Protein Domain Annotator's output, so you can paste positions straight across. Not every UniProt accession has a prediction; the tool reports that plainly rather than as an error. Structure coordinates are fetched directly from AlphaFold's own CDN, and the accession you look up is never logged or stored.
Only have a gene symbol? Resolve it to a UniProt accession first →
For an accession lookup, only the UniProt accession is sent to the SeqBench API to fetch a small metadata record from AlphaFold DB, and structure coordinates are fetched directly by your browser from AlphaFold's own CDN. For a sequence fold, your pasted sequence is sent directly from your browser to the public ESM Metagenomic Atlas API, not to SeqBench's own server. A structure file you open is read and drawn in your browser; the file itself is not sent to SeqBench. The metadata lookup (alphafold_lookup) and the file reader (parse_structure) are also available via the REST API and the MCP server.
How to use the AlphaFold Structure Viewer tool
- 1Drop a .pdb or .cif file (a .gz, or the .zip AlphaFold Server gives you, works too) — or enter a UniProt accession (e.g. P04637) and click Look up.
- 2Read the chain table under the 3D view: sequences, residues without coordinates, ligands, mass/pI/ε280 and, for a model, pLDDT. Download every chain as FASTA.
- 3Add one or more residue ranges (start–end, 1-based inclusive, plus an optional label) to highlight a domain, mutation or region of interest in its own color on the structure.
Frequently asked questions
What does opening a PDB or mmCIF file show?
The structure in 3D, and under it one row per chain: its sequence as deposited (copy it, or download every chain as FASTA), which stretches have no coordinates, molecular mass, pI and ε280 for protein chains, bound ligands by name and copy number, and the experimental method and resolution. For a model from AlphaFold DB, AlphaFold Server, ColabFold or ESMFold it also gives the mean pLDDT and the stretches below 50 — but only when the file itself marks its B-factor column as confidence, so an experimental structure's B-factors are never read as pLDDT.
Is my structure file uploaded?
No. The file is read and drawn in your browser; nothing is sent to SeqBench to open it. Only the first model of a multi-model (NMR) file is read.
Why do some accessions show "no prediction found"?
AlphaFold DB covers roughly 214 million structures across essentially all of UniProt, so a missing prediction usually isn't about obscurity — it genuinely means no model exists for that exact accession (this does happen). Double-check the accession is a canonical UniProt entry, e.g. via the Gene ID Mapper, rather than assuming the protein is simply too obscure to be covered.
What do the structure colors mean?
An AlphaFold DB lookup is colored by AlphaFold's per-residue confidence (pLDDT), from dark blue (very high confidence) through yellow to orange (low confidence) — AlphaFold's own standard scheme, applied automatically. A file you open is colored by chain; its pLDDT, where the file has one, is in the chain table. Any residue range you add is highlighted on top in its own distinct color.
What does the residue range use — 1-based or 0-based positions?
1-based inclusive, matching standard UniProt numbering and the Protein Domain Annotator's {start, end} output — so you can paste a domain's reported position directly into a highlight range without converting it.
Can I reuse an AlphaFold DB structure?
Yes — AlphaFold DB data is CC-BY 4.0 licensed; cite AlphaFold DB when reusing a structure.