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polaris: Skill for Claude Code

.claude/skills/foldseek_structural_search/SKILL.md

foldseek-structural-search is a skill for Claude Code from BeyondTheProtocol/polaris. It costs 97 tokens per session (1,286 once invoked), scanned A, original, AGPL-3.0.

A tool for searching protein databases by three-dimensional shape using Foldseek. It compares a supplied structure file, such as PDB or mmCIF, with structures from sources including PDB and AlphaFold.

In plain words
What is it for?
Use it when you have a protein coordinate file and want structurally similar proteins from public structure databases.
Why use it?
It helps find proteins with similar shapes when sequence similarity is not enough or is not the question being asked.

Skill for Claude Code

Written for Claude Code: installed under .claude/.

This is BeyondTheProtocol/polaris's own configuration. It tells Claude Code how to work on polaris itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything polaris configures →

not rated 49repo 21d ago A scan 97 tokens AGPL-3.0
View source ↗ BeyondTheProtocol/polaris
Reuse

Borrowing it

Nothing to install: this file belongs to BeyondTheProtocol/polaris. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/BeyondTheProtocol/polaris/master/.claude/skills/foldseek_structural_search/SKILL.md
Clone the repo
git clone --depth 1 https://github.com/BeyondTheProtocol/polaris

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for foldseek-structural-search

README.md
[![agentmods](https://agentmods.dev/badge/skills/beyondtheprotocol/polaris/foldseek_structural_search/github.svg)](https://agentmods.dev/skills/beyondtheprotocol/polaris/foldseek_structural_search)
Your own site
<a href="https://agentmods.dev/skills/beyondtheprotocol/polaris/foldseek_structural_search"><img src="https://agentmods.dev/badge/skills/beyondtheprotocol/polaris/foldseek_structural_search/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for foldseek-structural-search

Your own site · 80×15
<a href="https://agentmods.dev/skills/beyondtheprotocol/polaris/foldseek_structural_search"><img src="https://agentmods.dev/badge/skills/beyondtheprotocol/polaris/foldseek_structural_search.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 97 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,286 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00097 $0.01286
Opus 5.5 $0.00039 $0.00514
Sonnet 5.5 $0.00019 $0.00257
Haiku 4.5 $0.00010 $0.00129

Measured yesterday against content hash 3aff6e5f4725, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

foldseek-structural-search scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured yesterday.

The scan reads SKILL.md. This mod also ships 1 executable file (scripts/search.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.claude/skills/foldseek_structural_search/SKILL.md · 100 lines

The source is not reproduced here

Licensed AGPL-3.0

The repository is licensed AGPL-3.0, which this catalogue does not treat as permission to reproduce the file. Read it at the source.

Read it on GitHub

Files

What ships with it

2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. yesterday First seen · 100 lines · 97 tokens per session scan A 3aff6e5f4725

Subscribe to this mod's changes

foldseek-structural-search is a skill published in the GitHub repository BeyondTheProtocol/polaris (49 stars, last pushed 21d ago), licensed AGPL-3.0. It adds 97 tokens to every session and 1,286 once invoked, about $0.0004 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-11-07.

Scientificagentic-systemsai-agentscancer-researchllm-orchestrationopen-science
Related

foldseek-structural-search compared with skills from other repositories

foldseek-structural-search next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
foldseek-structural-searchBeyondTheProtocol/polarisSkill4921d agoAGPL-3.0A97Claude Code
remote-compute-sshaipoch/open-scienceSkill5.5ktodayApache-2.0A53Claude Code, Codex
figure-styleaipoch/open-scienceSkill5.5ktodayApache-2.0A91Claude Code, Codex
paper-narrativeaipoch/open-scienceSkill5.5ktodayApache-2.0A58Claude Code, Codex
figure-composeraipoch/open-scienceSkill5.5ktodayApache-2.0A93Claude Code, Codex
literature-reviewaipoch/open-scienceSkill5.5ktodayApache-2.0A54Claude Code, Codex
scvi-toolsaipoch/open-scienceSkill5.5ktodayApache-2.0A100Claude Code, Codex