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alphafold-db

Access over 200M protein structures from AlphaFold DB; use when you need to retrieve predicted 3D structures (PDB/mmCIF), confidence metrics (pLDDT/PAE), or protein metadata by UniProt accession.

Published by aipoch ↗aipoch/medical-research-skills

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alphafold-db

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Use alphafold-db to retrieve the predicted structure, confidence metrics, and metadata for UniProt accession [accession] in [PDB or mmCIF] format, saving the resulting files to [output directory].

Required inputs

  • [accession]
  • [PDB or mmCIF]
  • [output directory]

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SKILL.md

name: alphafold-dbdescription: Access over 200M protein structures from AlphaFold DB; use when you need to retrieve predicted 3D structures (PDB/mmCIF), confidence metrics (pLDDT/PAE), or protein metadata by UniProt accession.license: MITauthor: AIPOCH

Source: https://github.com/aipoch/medical-research-skills

AlphaFold Database Skill

When to Use

  • You have a UniProt accession (e.g., P00520) and need to download its AlphaFold-predicted 3D structure in mmCIF or PDB format.
  • You want to assess prediction reliability using per-residue pLDDT confidence scores.
  • You need PAE (Predicted Aligned Error) data to support domain-level interpretation or inter-domain confidence checks.
  • You want to programmatically retrieve AlphaFold DB metadata (e.g., model/structure URLs and related fields) for downstream pipelines.
  • You are building an automated workflow that fetches structures + confidence metrics for many proteins by UniProt ID.

Key Features

  • Fetch AlphaFold DB predicted structures by UniProt accession.
  • Download structure files in mmCIF (default) or PDB.
  • Retrieve and save metadata JSON, including confidence-related fields (e.g., pLDDT) and URL information.
  • Simple CLI workflow suitable for scripting and batch processing.

Dependencies

  • Python >=3.8
  • requests >=2.25

Example Usage

Fetch the structure and metadata for a UniProt ID and save them to a directory:

python scripts/fetch_structure.py --uniprot_id P00520 --output_dir ./out --format cif

Fetch as PDB instead:

python scripts/fetch_structure.py --uniprot_id P00520 --output_dir ./out --format pdb

Expected outputs in ./out:

  • P00520.cif (or P00520.pdb)
  • P00520_metadata.json (includes confidence/URL fields such as pLDDT-related information)

Implementation Details

  • Input identifier: UniProt accession ID (e.g., P00520).
  • Formats:
    • --format cif (default): downloads an mmCIF structure file.
    • --format pdb: downloads a PDB structure file.
  • Artifacts written:
    • Structure file named <UNIPROT_ID>.<cif|pdb>.
    • Metadata JSON named <UNIPROT_ID>_metadata.json, used to store confidence metrics (e.g., pLDDT) and AlphaFold DB URL-related fields.
  • API reference: Endpoint and response details are documented in references/api_reference.md.