Performs 3D structural searches of proteins against various databases (PDB, AlphaFold, CATH, MGnify, etc.) using the Foldseek API. Use ONLY when the user provides a physical 3D coordinate file (.cif, .mmcif, or .pdb) and wants to find structurally similar proteins.
SkillScore36Maintained
Automatic
◆Research pack
Last verified 8/21/2026
What it changes
Passed 4 of 10 test cases with the skill, and 3 of 10 without it.
Without skill27%
With skill36%
Checks it passed that the model alone missed
Uses `uv run` to execute the Python script.
States the file path of the generated JSON output file.
States the file path of the generated Markdown summary file.
and 2 more in the full report
3 fixed5 passed either way13 still failing1 broke
Pass-rate lift
+9 pp
Tokens
+36%
Agent turns
0%
Response time
-30%
Model gemini-3.6-flashMeasured 8/21/2026v18 of 22 cases passed with skill · 10 comparable
Tokens, turns and time describe resource use, not a dollar price.
See it in action
One of 3 test cases the skill fixed. Same model, same prompt, with and without the skill.
1 of 3
Prompt
What Python execution wrapper must be used when launching `scripts/search.py`?
What was checked, without and with the skill
Checked
Without skill
With skill
Uses `uv run` to execute the Python script.
Missed
Passed
case-21 · 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.md89 lines2 filesincludes scripts
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://search.foldseek.com/search and
https://github.com/steineggerlab/foldseek, then (2) create the file
recording the notification text and timestamp.
Goal
Submit a user-provided 3D protein structure file (.cif, .mmcif, or .pdb)
to the Foldseek web server API to find structurally similar proteins. Report the
top structural hits, interpret key alignment metrics, summarize the inferred
protein functions, save the Markdown-formatted table to a .md file, and save
the full detailed results to a local JSON file.
Core Rules
File Requirement: This tool absolutely cannot search by sequence, name,
or accession ID. It strictly requires a .pdb, .cif, or .mmcif file
path.
Strict Validation: Never bypass the input validation or the database
allowlist check.
Do Not Parse the JSON: Rely entirely on the generated .md file for
your immediate summary. The JSON is saved purely for subsequent, specialized
tool use.
No Raw Parsing: Do not attempt to parse or read the raw 3D coordinates
yourself; always pass the file to the script.
Notification: If this skill is used, ensure this is mentioned in the
output.
Instructions
Strict Input Validation: Verify that the user has explicitly provided a
valid path to a .cif, .mmcif, or .pdb file in their workspace.
If the user provided a protein name, an amino acid sequence, or an
accession ID (e.g., a UniProt ID) but NO downloaded structure file,
halt immediately. Do not run the script.