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Medical-research-skills 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.

install
source · Clone the upstream repo
git clone https://github.com/aipoch/medical-research-skills
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/aipoch/medical-research-skills "$T" && mkdir -p ~/.claude/skills && cp -r "$T/scientific-skills/Evidence Insight/alphafold-db" ~/.claude/skills/aipoch-medical-research-skills-alphafold-db && rm -rf "$T"
manifest: scientific-skills/Evidence Insight/alphafold-db/SKILL.md
source content

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
    .