AlphaFold inputs
Give Ivy one input, a UniProt accession like P00533 — entry names, gene symbols and PDB IDs do not resolve, and isoforms are canonical only.
You provide one thing: a UniProt accession for the protein you want. Getting that accession right is what most affects the result — an entry name, gene symbol, or PDB ID won't resolve directly, and whether a structure comes back at all depends on the protein being covered by the AlphaFold Database.
Inputs
You ask for an AlphaFold structure in chat; the lookup needs one thing, a UniProt accession. There is no form or job for it.
UniProt accession (required)
A UniProt accession, e.g. P00533 (human EGFR), P68871 (hemoglobin subunit beta), Q9Y6K9 (NEMO).
Accepted formats
| Form | Example | Accepted |
|---|---|---|
| UniProt accession | P00533 | ✓ |
| UniProt entry name | EGFR_HUMAN | ⚠︎ Ivy resolves it to an accession first with a UniProt search |
| PDB ID | 6LU7 | ✗ Ask for the PDB entry instead |
| Raw sequence | MKTAY... | ✗ Ask for an ESMFold prediction instead |
| Gene symbol | EGFR | ✗ Ivy resolves it with a UniProt search first |
If you have a gene name or protein name rather than an accession, just ask in chat — Ivy runs a UniProt search, then the AlphaFold fetch, automatically.
How to find a UniProt accession
- By name: in chat, "Find UniProt entry for EGFR" → runs a UniProt search
- By BLAST: provide a sequence and BLAST returns the closest UniProt hits
- Manually: search at uniprot.org
Database coverage limits
Not every UniProt entry has an AlphaFold structure. The database covers:
- All reviewed (Swiss-Prot) human entries
- Most reviewed entries from major model organisms
- A large subset of TrEMBL (unreviewed) entries for covered proteomes
If the fetch returns "not found":
- Ask Ivy to predict it with ESMFold from the UniProt sequence instead
- Or ask in one message to try AlphaFold first and fall back to ESMFold; the orchestrator chains both
What the AlphaFold fetch does NOT take
- Custom sequences — the fetch only looks up pre-computed structures. For novel or mutated sequences, ask for an ESMFold prediction.
- Multi-chain complexes — a UniProt entry in the AlphaFold DB is a single chain, modelled alone, with no partners, ligands, ions or cofactors. For multimers, use a co-folding model (Boltz-2, Chai-1) or AlphaFold-Multimer via a different workflow. Published AlphaFold figures on complexes almost always describe AlphaFold-Multimer, which is not what this tool returns — see translatability.
- Specific isoforms beyond canonical — the fetch returns the database's
F1entry for the accession. Non-canonical isoforms need an ESMFold prediction on the isoform sequence.
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AlphaFold quickstart
Fetch a pre-computed AlphaFold structure by UniProt ID in 2-5 seconds, no GPU — pLDDT-colored canvas card, downloadable PDB, ESMFold fallback on a miss.
AlphaFold troubleshooting
Recover from a structure-not-found miss, a case-sensitive UniProt ID, EBI outages, red low-pLDDT regions, and a result that is one chain with no ligands.