Agent skill · research science · google-deepmind
alphafold-database-fetch-and-analyze
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 sequence — ask for a UniProt ID first.
Why this skill is useful
Adds executable scripts for fetching and analyzing AlphaFold structural data that the AI wouldn't reliably generate on its own.
What it needs
Requires uv installed locally. About 3k tokens when loaded. Last updated 2026-07-07. 2,648 stars on the source repository.
What this skill does
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/alphafolddatabasefetchandanalyzeLICENSE.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, predictedalignederror.json, and API metadata JSON (-metadata.json) for a UniProt ID. Handles fragment fallback for very large proteins. Examples: 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. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills google-deepmind/alphafold_database_fetch_and_analyze