alphafold-structure-prediction

alphafold-structure-prediction is a skill for Claude Code, Codex from Pavel-Kravchenko/Bioinformatics. It costs 110 tokens per session (2,770 once invoked), scanned B, original, no licence file.

Tools and guidance for predicting a protein’s three-dimensional shape from its amino-acid sequence. They also cover existing AlphaFold Database models and confidence measures such as pLDDT and PAE.

In plain words
What is it for?
Use them to predict a structure with AlphaFold2, ColabFold, or ESMFold, download a precomputed model, or interpret model-confidence metrics and Cα RMSD.
Why use it?
They help researchers obtain or assess predicted protein structures and understand how reliable different parts of a model may be.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

Good fit Use them to predict a structure with AlphaFold2, ColabFold, or ESMFold, download a precomputed model, or interpret model-confidence metrics and Cα RMSD.

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Install with agentmods
npx agentmods add skills/pavel-kravchenko/bioinformatics/alphafold-structure-prediction
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.

Any agent
npx skills add Pavel-Kravchenko/Bioinformatics --skill alphafold-structure-prediction
Clone the repo
git clone --depth 1 https://github.com/Pavel-Kravchenko/Bioinformatics

Made for: Claude Code, Codex.

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-structure-prediction

README.md
[![agentmods](https://agentmods.dev/badge/skills/pavel-kravchenko/bioinformatics/alphafold-structure-prediction/github.svg)](https://agentmods.dev/skills/pavel-kravchenko/bioinformatics/alphafold-structure-prediction)
Your own site
<a href="https://agentmods.dev/skills/pavel-kravchenko/bioinformatics/alphafold-structure-prediction"><img src="https://agentmods.dev/badge/skills/pavel-kravchenko/bioinformatics/alphafold-structure-prediction/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 alphafold-structure-prediction

Your own site · 80×15
<a href="https://agentmods.dev/skills/pavel-kravchenko/bioinformatics/alphafold-structure-prediction"><img src="https://agentmods.dev/badge/skills/pavel-kravchenko/bioinformatics/alphafold-structure-prediction.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 110 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,770 The whole file, excluding the scripts and references it only reads on demand.
Security scan B 2 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 $0.00110 $0.02770
Opus 5 $0.00055 $0.01385
Sonnet 5 $0.00022 $0.00554
Haiku 4.5 $0.00011 $0.00277

Measured 12d ago against content hash b6dd92fc54af, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade B, and why

alphafold-structure-prediction scanned grade B 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 12d 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.

Sends data to an external URLmediumData exfiltration

A POST to an outside endpoint may be telemetry or may be exfiltration; either way the mod talks to somewhere, and you should know where.

resp = requests.post( "https://api.esmatlas.com/foldSequence/v1/pdb/",

Makes network callslowCapability

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

resp = requests.get(url, timeout=30)
Skills/alphafold-structure-prediction/SKILL.md · 238 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

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. 12d ago First seen · 238 lines · 110 tokens per session scan B b6dd92fc54af

Subscribe to this mod's changes

alphafold-structure-prediction is a skill published in the GitHub repository Pavel-Kravchenko/Bioinformatics (5 stars, last pushed 2mo ago), with no licence file. It adds 110 tokens to every session and 2,770 once invoked, about $0.0006 per session on Opus 5. A static security scan graded it B with 2 findings (sends data to an external url, makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.