Retrieve and analyze AlphaFold predicted structures for a protein.
SkillScore68Maintained
Automatic
◆Research pack
Last verified 8/21/2026
What it changes
Passed 12 of 18 test cases with the skill, and 6 of 18 without it.
Without skill32%
With skill68%
Checks it passed that the model alone missed
Specifies using uv run to execute the Python scripts.
Directs the user to look up the accession code on UniProt.
Declines to run structure fetching without a UniProt identifier.
and 8 more in the full report
8 fixed7 passed either way7 still failing0 broke
Pass-rate lift
+36 pp
Tokens
+11%
Agent turns
0%
Response time
-36%
Model gemini-3.6-flashMeasured 8/21/2026v115 of 22 cases passed with skill · 18 comparable
Tokens, turns and time describe resource use, not a dollar price.
See it in action
One of 8 test cases the skill fixed. Same model, same prompt, with and without the skill.
1 of 8
Prompt
I have 'AF-P00520-F1-predicted_aligned_error_v6.json' saved in './data/'. What exact shell command executes the PAE and domain boundary analysis tool on this file?
What was checked, without and with the skill
Checked
Without skill
With skill
Invokes uv run scripts/analyze_pae.py with the PAE JSON file path.
Missed
Passed
case-16 · gemini-3.6-flash · 8/21/2026 · answers are capped and redacted
What's inside
The instructions your model reads when the skill loads.
SKILL.md105 lines4 filesincludes scripts
AlphaFold Database: Fetch and Analyze
Prerequisites
uv: Read the uv skill and follow its Setup instructions to ensure
uv is installed and on PATH.
User Notification: If LICENSE_NOTIFICATION.txt does not already exist in
this skill 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.