AlphaFold Structure Lookup

Get AlphaFold DB predicted structures for UniProt accessions with confidence metrics (mean pLDDT, confidence class, per-band fractions) and direct PDB/mmCIF/PAE download links.

Why use it

• Triage which targets have trustworthy predicted models
• Batch-download model links for docking or design pipelines
• Compare predicted vs. experimental coverage (combine with PDB Structure Lookup)

No API keys, no scraping of HTML – the actor talks to the official public API, handles paging, rate limits and retries, and returns flat JSON you can export as CSV/Excel or call from code, Make, Zapier, n8n or AI agents (Apify MCP server).

Input

Field	Title	Description
uniprotAccessions	UniProt accessions	e.g. P04637, Q9NQS5.
minMeanPlddt	Minimum mean pLDDT	Optional: only return models at or above this mean pLDDT (0-100).
includeIsoforms	Include isoform models	Also return AlphaFold models of UniProt isoforms (e.g. P04637-9). Default: canonical sequence only.

Example input:

{
  "uniprotAccessions": [
    "P04637",
    "Q9NQS5"
  ],
  "includeIsoforms": false
}

Output (one dataset item per result)

{
  "uniprotAccession": "P04637",
  "entryId": "AF-P04637-F1",
  "gene": "TP53",
  "meanPlddt": 75.06,
  "confidenceClass": "confident",
  "fractionPlddtVeryHigh": 0.527,
  "pdbUrl": "https://alphafold.ebi.ac.uk/files/AF-P04637-F1-model_v6.pdb"
}

Use with AI agents (Apify MCP server)

Add the Apify MCP server (https://mcp.apify.com) to Claude, Cursor or any MCP client and enable this actor (researchdata/alphafold-structure-lookup). The agent can then call it directly: describe what you need, the agent fills the input fields above, runs the actor and reads the dataset. Because results are flat JSON with explicit nulls, an agent can use them without extra parsing. Set a maximum cost per run to keep agent calls capped.

Pricing

Pay per event: $0.002 per result (prediction returned). You only pay for results you get; set a max cost per run to cap spending. Higher Apify plans get automatic volume discounts: Bronze −10 %, Silver −20 %, Gold −30 %.

Cost example

At $0.002 per result: 50 results ≈ $0.10, 1,000 results ≈ $2.00. Set a maximum cost per run in the run options to cap spending.

Limits

• Data comes from the provider's public API; fields the provider does not publish are returned empty (null), never guessed.
• Results reflect the provider's database at run time.
• Not affiliated with the data provider.
• AlphaFold models are predictions, not experimental structures.

FAQ

What does pLDDT mean?
A per-residue confidence score of the prediction; the actor reports the mean and the share of residues per confidence band.

How do I compare predicted and experimental coverage?
Combine it with PDB Structure Lookup.

Data source & terms

AlphaFold Protein Structure Database, EMBL-EBI (CC BY 4.0). Please respect the data provider's terms and cite the original resource in publications. This actor is an independent tool and is not affiliated with or endorsed by the data provider.