AlphaFold DB
The AlphaFold Protein Structure Database holds predicted 3D protein structures and is run by Google DeepMind and EMBL-EBI. Through ScholarMuse, an agent can fetch the predicted model for a UniProt accession and read its confidence scores and file links. The model is returned next to the experimental PDB entries for the same protein, so the two can be compared in one call.
ScholarMuse tools: get_structure. Each successful call uses credits.
Ask your agent
What your agent gets back
Every record carries id, source, title, url, license, attribution and retrievedAt. The fields below are the data that comes from AlphaFold DB.
get_structure
One record with kind "predicted", only when a UniProt accession is known and AlphaFold DB has a model for it.
- entryId
- AlphaFold DB entry id, e.g. AF-P00533-F1
- uniprotId
- UniProt accession of the model
- gene
- Gene name
- organism
- Organism scientific name
- meanPlddt
- Mean pLDDT confidence score
- fractionVeryHighConfidence
- Fraction of residues with very high pLDDT
- fractionLowConfidence
- Fraction of residues with low pLDDT
- version
- Latest model version
- modelDate
- Date the model was created
- residueStart
- First UniProt residue covered
- residueEnd
- Last UniProt residue covered
- mmcifUrl
- mmCIF file download link
- paeImageUrl
- Predicted aligned error image link
What it covers
- Predicted protein structures in AlphaFold DB, looked up one UniProt accession at a time.
- One model per call: the one for the canonical sequence. The isoformModels field counts the other models AlphaFold DB returned.
- When you pass a PDB id, the model returned is for the first UniProt accession listed in that entry.
Limits
- AlphaFold DB cannot be searched by name here. A name works only when it exactly matches a human gene symbol or protein name in UniProt; otherwise no predicted model is returned.
- Returns confidence summaries and file links, not coordinates or per-residue pLDDT values.
- Proteins without a model in AlphaFold DB return nothing from this source.
How ScholarMuse reaches AlphaFold DB
The connector calls the AlphaFold DB API at alphafold.ebi.ac.uk/api/prediction/{UniProt accession}. No API key is sent.
Responses are cached for up to 7 days, so a new model version can take that long to appear.
API key: the upstream API can be called without one, so you do not add one.
Licence and attribution
Licence: CC BY 4.0
Predicted structure from AlphaFold Protein Structure Database (alphafold.ebi.ac.uk), Google DeepMind and EMBL-EBI, CC BY 4.0.
Records that come from AlphaFold DB carry this licence and attribution. When you cite the data in a paper, follow AlphaFold DB's own citation guidance.
