alphafold-database-fetch-and-analyze

1# AlphaFold Database: Fetch and Analyze
2 
3## Prerequisites
4 
51.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
6    `uv` is installed and on PATH.
72.  **User Notification**: If
8    .licenses/alphafold_database_fetch_and_analyze_LICENSE.txt does not already
9    exist in the workspace root directory then (1) prominently notify the user
10    to check the terms at https://alphafold.ebi.ac.uk/, then (2) create the file
11    recording the notification text and timestamp.
12 
13## Overview
14 
15Downloads AlphaFold predicted structures (mmCIF) and Predicted Aligned Error
16(PAE) matrices from the AlphaFold Database for a given UniProt ID, then performs
17automated heuristic analysis on structural confidence (pLDDT), intrinsically
18disordered regions, rigid domain boundaries, and inter-domain flexibility.
19 
20**Do NOT use when:**
21 
22-   The user only has a protein name, gene name, or amino acid sequence (no
23    UniProt ID) — ask them to look up the ID on
24    [UniProt](https://www.uniprot.org).
25-   The user wants to search for structural homologs (use **Foldseek**).
26-   The user wants to run AlphaFold predictions on a custom sequence.
27-   The user needs experimental PDB structures (use **RCSB PDB**).
28 
29## Core Rules
30 
31-   **Use the Wrapper**: ALWAYS execute the provided helper scripts to query the
32    database rather than accessing the database directly. The scripts
33    automatically enforce the required rate limit gracefully.
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