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polaris: Skill for Claude Code

.claude/skills/pdb_database/SKILL.md

pdb-database is a skill for Claude Code from BeyondTheProtocol/polaris. It costs 61 tokens per session (2,305 once invoked), scanned A, original, AGPL-3.0.

A research tool for the Protein Data Bank, a public collection of experimentally determined three-dimensional structures of proteins and other biomolecules.

In plain words
What is it for?
Finding or downloading biomolecular structures, searching by sequence or structure similarity, and retrieving experiment information.
Why use it?
It helps locate structural experiments and related molecules using biological and chemical search details.

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 61 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/pdb_database/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 pdb-database

README.md
[![agentmods](https://agentmods.dev/badge/skills/beyondtheprotocol/polaris/pdb_database/github.svg)](https://agentmods.dev/skills/beyondtheprotocol/polaris/pdb_database)
Your own site
<a href="https://agentmods.dev/skills/beyondtheprotocol/polaris/pdb_database"><img src="https://agentmods.dev/badge/skills/beyondtheprotocol/polaris/pdb_database/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 pdb-database

Your own site · 80×15
<a href="https://agentmods.dev/skills/beyondtheprotocol/polaris/pdb_database"><img src="https://agentmods.dev/badge/skills/beyondtheprotocol/polaris/pdb_database.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 61 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,305 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 1 finding. 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 $0.00061 $0.02305
Opus 5.5 $0.00024 $0.00922
Sonnet 5.5 $0.00012 $0.00461
Haiku 4.5 $0.00006 $0.00231

Measured yesterday against content hash 9d5f96f75127, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

pdb-database scanned grade A with 1 finding 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 4 executable files (scripts/download_coordinate_files.py, scripts/fetch_pdb_metadata.py, scripts/fetch_schema.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.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

`curl`, `urllib`, raw HTTP requests, or any other method to access PDB APIs.
.claude/skills/pdb_database/SKILL.md · 170 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

5 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 · 170 lines · 61 tokens per session scan A 9d5f96f75127

Subscribe to this mod's changes

pdb-database is a skill published in the GitHub repository BeyondTheProtocol/polaris (49 stars, last pushed 21d ago), licensed AGPL-3.0. It adds 61 tokens to every session and 2,305 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-11-07.

DatabasesScientificagentic-systemsai-agentscancer-researchllm-orchestrationopen-science
Related

pdb-database compared with skills from other repositories

pdb-database next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
pdb-databaseBeyondTheProtocol/polarisSkill4921d agoAGPL-3.0A61Claude Code
tiledbvcfK-Dense-AI/scientific-agent-skillsSkill56k6d agoMITA62Claude Code, Codex
lamindbK-Dense-AI/scientific-agent-skillsSkill56k6d agoMITA58Claude Code, Codex
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