alphafold-database

alphafold-database is a skill for Claude Code, Codex from jimmc414/Kosmos. It costs 55 tokens per session (3,898 once invoked), scanned A, original, no licence file.

A way to retrieve AI-predicted protein structures from the AlphaFold database, which stores estimated three-dimensional shapes for proteins.

In plain words
What is it for?
Looking up structures by UniProt ID, downloading PDB or mmCIF files, and checking confidence measures such as pLDDT and PAE for drug discovery or structural biology.
Why use it?
It lets researchers examine predicted protein shapes and their reliability without determining every structure experimentally.

Skill for Claude CodeCodex

Part of the scientific-skills plugin — 119 skills shipped together

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods
npx agentmods add skills/jimmc414/kosmos/alphafold-database
Any agent
npx skills add jimmc414/Kosmos --skill alphafold-database
Clone the repo
git clone --depth 1 https://github.com/jimmc414/Kosmos

Made for: Claude Code, Codex.

Or install scientific-skills, the plugin that ships this one along with the rest of its 119 skills.

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 alphafold-database

README.md
[![agentmods](https://agentmods.dev/badge/skills/jimmc414/kosmos/alphafold-database.svg)](https://agentmods.dev/skills/jimmc414/kosmos/alphafold-database)
Your own site
<a href="https://agentmods.dev/skills/jimmc414/kosmos/alphafold-database"><img src="https://agentmods.dev/badge/skills/jimmc414/kosmos/alphafold-database.svg" alt="Measured on agentmods" height="20"></a>
Per session 55 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 3,898 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 2 findings. Scan, not verified.
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 $0.00055 $0.03898
Opus 5 $0.00028 $0.01949
Sonnet 5 $0.00011 $0.00780
Haiku 4.5 $0.00006 $0.00390

Measured 4d ago against content hash 9c9f982059f6, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

alphafold-database scanned grade A with 2 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 4d ago.

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.

response = requests.get(api_url)

Runs shell commandslowCapability

Expected in a hook, worth knowing in a rule or an instructions file.

subprocess.run(cmd, shell=True, check=True)
kosmos-claude-scientific-skills/scientific-skills/alphafold-database/SKILL.md · 501 lines

The source is not reproduced here

No licence file

A repository with no LICENSE is all rights reserved by default, so the body is not copied here. The metadata, the measurements and the link are.

Read it on GitHub

Files

What ships with it

1 file 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. 4d ago First seen · 501 lines · 55 tokens per session scan A 9c9f982059f6

Subscribe to this mod's changes

alphafold-database is a skill published in the GitHub repository jimmc414/Kosmos (577 stars, last pushed 5mo ago), with no licence file. It adds 55 tokens to every session and 3,898 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 2 findings (makes network calls, runs shell commands). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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