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alphafold-database-fetch-and-analyze

google-deepmind · Бази данни

Retrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Accession ID and wants structural confidence metrics (pLDDT), domain boundary analysis, or disorder assessment. Do not use if the user only has a protein name, gene name, or amino acid se

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Платформи: Не са посочениНиво: Не е посоченоВ индекса: 22.09.2026 г.Обновен в GitHub: 15.09.2026 г.

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22.09.2026 г.

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AlphaFold Database: Fetch and Analyze

Prerequisites

  1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
  2. User Notification: If .licenses/alphafold_database_fetch_and_analyze_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://alphafold.ebi.ac.uk/, then (2) create the file recording the notification text and timestamp.

Overview

Downloads AlphaFold predicted structures (mmCIF) and Predicted Aligned Error (PAE) matrices from the AlphaFold Database for a given UniProt ID, then performs automated heuristic analysis on structural confidence (pLDDT), intrinsically disordered regions, rigid domain boundaries, and inter-domain flexibility.

Do NOT use when:

  • The user only has a protein name, gene name, or amino acid sequence (no UniProt ID) — ask them to look up the ID on UniProt.
  • The user wants to search for structural homologs (use Foldseek).
  • The user wants to run AlphaFold predictions on a custom sequence.
  • The user needs experimental PDB structures (use RCSB PDB).

Core Rules

  • Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully.
  • Do not attempt to calculate domain boundaries or assess structural disorder yourself; always rely on the output provided by the script.
  • If this skill is used, ensure this is mentioned in the output.

Utility Scripts

1. Fetch Structure Files

Downloads the .cif structure file, _predicted_aligned_error.json, and API metadata JSON (-metadata.json) for a UniProt ID. Handles fragment fallback for very large proteins.

Examples:

uv run scripts/fetch_structure.py P00520 -o /path/to/output/
uv run scripts/fetch_structure.py P04637 -o /path/to/custom_results/

Always specify -o with an absolute path or a path relative to the user's project root, never a path relative to the skill directory.

2. Analyze pLDDT Confidence

Reads pLDDT confidence metrics from a saved AFDB metadata JSON file (produced by fetch_structure.py) and prints a heuristic confidence assessment (structured, disordered, mixed).

Example:

uv run scripts/analyze_plddt.py ./data/AF-P00520-F1-metadata.json

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