What is alphafold3_mcp CLAUDE.md?

Project-specific instructions for working on MacromNex's alphafold3_mcp code repository. They cover the project, common commands, starting its MCP server, and running tests.

Use them when modifying, testing, or running the alphafold3_mcp project.

They give a coding agent the repository context and commands needed to work on the project correctly.

How MacromNex/alphafold3_mcp configures Claude Code

Reuse

Borrowing it

Nothing to install: this file belongs to MacromNex/alphafold3_mcp. 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/MacromNex/alphafold3_mcp/main/CLAUDE.md

Clone the repo

git clone --depth 1 https://github.com/MacromNex/alphafold3_mcp

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.

README.md

[![agentmods](https://agentmods.dev/badge/instructions/macromnex/alphafold3_mcp/claude-md/github.svg)](https://agentmods.dev/instructions/macromnex/alphafold3_mcp/claude-md)

Your own site

<a href="https://agentmods.dev/instructions/macromnex/alphafold3_mcp/claude-md"><img src="https://agentmods.dev/badge/instructions/macromnex/alphafold3_mcp/claude-md/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.

Your own site · 80×15

<a href="https://agentmods.dev/instructions/macromnex/alphafold3_mcp/claude-md"><img src="https://agentmods.dev/badge/instructions/macromnex/alphafold3_mcp/claude-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 1,023 This file is loaded in full into every session.

When invoked 1,023 The same file — it is already loaded in full.

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.

Model	Per session	Once invoked
Fable 5.1	$0.01023	$0.01023
Opus 5.5	$0.00409	$0.00409
Sonnet 5.5	$0.00205	$0.00205
Haiku 4.5	$0.00102	$0.00102

Measured 2mo ago against content hash ad0e6c0b71b0, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

alphafold3_mcp CLAUDE.md 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 2mo 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.

Runs shell commandslowCapability

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

**Tool execution model**: Tools shell out to AlphaFold3 runner scripts (`run_alphafold.py`, `run_alphafold_with_a3m.py`, `run_alphafold_with_a3m_batch.py`) via `subprocess.Popen`. Real-time log streaming is handled by `_

CLAUDE.md · 72 lines

The source is not reproduced here

No licence file

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.

2mo ago First seen · 72 lines · 1,023 tokens per session scan A ad0e6c0b71b0

Subscribe to this mod's changes

alphafold3_mcp CLAUDE.md is an instructions file published in the GitHub repository MacromNex/alphafold3_mcp (2 stars, last pushed 1mo ago), with no licence file. It adds 1,023 tokens to every session, about $0.0041 per session on Opus 5.5. A static security scan graded it A with 1 finding (runs shell commands). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

alphafold bioinformatics deep-learning mcp model-context-protocol protein-engineering

alphafold3_mcp CLAUDE.md next to 6 instructions from other repositories
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vscode copilot-instructions.mdmicrosoft/vscode	Instructions file	195k	yesterday	MIT	A	3,093	GitHub Copilot
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alphafold3_mcp: Instructions file for Claude Code

Borrowing it

Wrote this? Show the measurements

What it costs to keep this loaded

Grade A, and why

Runs shell commandslowCapability

The source is not reproduced here

No licence file

What this file has done since we first saw it

alphafold3_mcp CLAUDE.md compared with instructions from other repositories