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.