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.
npx agentmods add instructions/macromnex/alphafold3_mcp/claude-mdgit clone --depth 1 https://github.com/MacromNex/alphafold3_mcpWrote 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.
[](https://agentmods.dev/instructions/macromnex/alphafold3_mcp/claude-md)<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="Measured on agentmods" height="20"></a>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 | $0.00511 | $0.00511 |
| Sonnet 5 | $0.00205 | $0.00205 |
| Haiku 4.5 | $0.00102 | $0.00102 |
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 5d 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 `_ 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.
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.
- 5d ago First seen · 72 lines · 1,023 tokens per session scan A ad0e6c0b71b0
alphafold3_mcp CLAUDE.md is an instructions file published in the GitHub repository MacromNex/alphafold3_mcp (1 stars, last pushed 5mo ago), with no licence file. It adds 1,023 tokens to every session, about $0.0051 per session on Opus 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.
Other instructions, from other repositories
boltzgen_mcp CLAUDE.md
Claude Code instructions for MacromNex/boltzgen_mcp, covering claude.md, what this is, setup, running and start mcp server.
boltz_mcp CLAUDE.md
Claude Code instructions for MacromNex/boltz_mcp, covering claude.md, what this is, setup, local (conda) and options: --skip-env, --skip-repo.
esmfold_mcp CLAUDE.md
Claude Code instructions for MacromNex/esmfold_mcp, covering claude.md, project overview, architecture, build & run commands and setup environments (automated).
spired_stab_mcp CLAUDE.md
Claude Code instructions for MacromNex/spired_stab_mcp, covering claude.md, what this is, common commands, activate environment and run mcp server.
chai1_mcp CLAUDE.md
Claude Code instructions for MacromNex/chai1_mcp, covering claude.md, project overview, architecture, key commands and setup (conda).
bindcraft_mcp CLAUDE.md
Claude Code instructions for MacromNex/bindcraft_mcp, covering claude.md, project overview, common commands, setup environment and run the mcp server.