# Alphafold Database Fetch And Analyze

Retrieve and analyze AlphaFold predicted structures for a protein.

- Repository: https://github.com/google-deepmind/science-skills (3377 stars)
- Category: Engineering
- License: Apache-2.0
- Last updated: 2026-10-23
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add google-deepmind/science-skills --skill alphafold-database-fetch-and-analyze -g -a claude-code -y`
Codex: `npx skills add google-deepmind/science-skills --skill alphafold-database-fetch-and-analyze -g -a codex -y`
Cursor: `npx skills add google-deepmind/science-skills --skill alphafold-database-fetch-and-analyze -g -a cursor -y`
Gemini CLI: `npx skills add google-deepmind/science-skills --skill alphafold-database-fetch-and-analyze -g -a gemini-cli -y`

## Description

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.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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](https://www.uniprot.org).
-   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:

The rest: https://github.com/google-deepmind/science-skills/blob/HEAD/skills/alphafold_database_fetch_and_analyze/SKILL.md