drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/database-lookup/references/alphafold.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
AlphaFold DB (Predicted Protein Structures)		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/alphafold.md	9c9bd2e9	2026-06-26	prompt	accepted	upstream	false

AlphaFold DB (Predicted Protein Structures)

Base URL

https://alphafold.ebi.ac.uk/api/

Auth

No auth required.

Key Endpoints

Endpoint	Description
/prediction/{uniprot_accession}	Prediction metadata by UniProt ID

Structure File URLs (direct download)

https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-model_v4.pdb
https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-model_v4.cif
https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-predicted_aligned_error_v4.json

Example Calls

# Get prediction metadata for EGFR
https://alphafold.ebi.ac.uk/api/prediction/P00533

# Download PDB structure
https://alphafold.ebi.ac.uk/files/AF-P00533-F1-model_v4.pdb

# Download PAE (predicted aligned error)
https://alphafold.ebi.ac.uk/files/AF-P00533-F1-predicted_aligned_error_v4.json

Response Format

JSON for metadata. PDB/mmCIF for structures. PAE as JSON matrix.

Rate Limits

No strict limits. Use FTP/Cloud for bulk downloads (~200M+ structures).