Borrowing it
Nothing to install: this file belongs to cyanheads/chembl-mcp-server. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/cyanheads/chembl-mcp-server/main/AGENTS.mdgit clone --depth 1 https://github.com/cyanheads/chembl-mcp-serverWrote 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/cyanheads/chembl-mcp-server/agents-md)<a href="https://agentmods.dev/instructions/cyanheads/chembl-mcp-server/agents-md"><img src="https://agentmods.dev/badge/instructions/cyanheads/chembl-mcp-server/agents-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.
<a href="https://agentmods.dev/instructions/cyanheads/chembl-mcp-server/agents-md"><img src="https://agentmods.dev/badge/instructions/cyanheads/chembl-mcp-server/agents-md.svg" alt="Reviewed on agentmods" width="80" 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 | $0.10564 | $0.10564 |
| Opus 5.5 | $0.04226 | $0.04226 |
| Sonnet 5.5 | $0.02113 | $0.02113 |
| Haiku 4.5 | $0.01056 | $0.01056 |
Grade A, and why
chembl-mcp-server AGENTS.md scanned grade A with 0 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 yesterday.
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.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
This is a copy
77% identical to obsidian-mcp-server AGENTS.md — 420 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 459 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Developer Protocol
Server: chembl-mcp-server
Version: 0.4.1
Framework: @cyanheads/mcp-ts-core ^0.13.15
Engines: Bun ≥1.4.0, Node ≥24.0.0
MCP SDK: @modelcontextprotocol/server ^2.3.1
Zod: ^4.6.7
Read the framework docs first:
node_modules/@cyanheads/mcp-ts-core/CLAUDE.mdcontains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
Server surface
ChEMBL drug-discovery data over the EBI REST API (https://www.ebi.ac.uk/chembl/api/data) — keyless, read-only. The curated compound ↔ target ↔ bioactivity link, plus drug mechanisms and indications.
Tools (src/mcp-server/tools/definitions/):
| Tool | Purpose |
|---|---|
chembl_search_molecules |
Discovery entry point — find compounds by name / ChEMBL ID / InChIKey, or structure search (exact / similarity / substructure) from a SMILES; every row names its family parent_chembl_id; a total at ChEMBL's name (10,000) or substructure (30,000) search ceiling comes back totalCountCapped; an unparseable similarity or substructure SMILES fails fast as invalid_structure |
chembl_search_targets |
Resolve a protein / gene / UniProt accession to the ChEMBL target ID chembl_get_bioactivities needs |
chembl_get_bioactivities |
Flagship compound↔target bridge — bioactivity measurements for a molecule, a target, or both (which narrows to that compound–target pair); include_alternate_forms widens the molecule to its family by parent; variant keeps wild-type measurements or one recorded mutant; potency_view picks the measurements with a derivable pchembl_value (default) or exactly those without one; large sets spill to a per-view DataCanvas table SQL'd via chembl_dataframe_query; whenever a call stages nothing (canvas off, or an inline fit with no canvas_id), cursor / nextCursor page through the view, and a cursor page never stages |
chembl_get_drug_info |
Drug pharmacology — mechanism(s) of action, target(s), first-approval year, clinical indications, read across the molecule's family (the parent its record resolves to, and that parent's salts and alternate forms) |
chembl_get_assay |
Assay provenance behind a bioactivity row — type, target, organism, 1–9 confidence score |
chembl_dataframe_query |
Read-only SQL SELECT over the staged bioactivity rows (canvas) |
chembl_dataframe_describe |
List tables/columns staged on a canvas before querying |
chembl_dataframe_drop |
Drop a staged table early. Opt-in behind CHEMBL_DATAFRAME_DROP_ENABLED; wrapped in disabledTool() when off, so it carries the enable hint in the manifest while staying absent from tools/list |
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.
- yesterday Changed · +11 lines · +490 tokens per session 23e4f999875c
- 8d ago Changed · +14 lines · +1,519 tokens per session 203ad1ca1e05
- 16d ago Changed · -1 lines · +59 tokens per session cffacf5bf094
- 29d ago Changed · +1 lines · +61 tokens per session 87c7ac6c556e
- 1mo ago Changed · +19 lines · +1,314 tokens per session 6c00f49108f0
- 1mo ago First seen · 415 lines · 7,121 tokens per session scan A 3eb9f11b9a76
chembl-mcp-server AGENTS.md is an instructions file published in the GitHub repository cyanheads/chembl-mcp-server (1 stars, last pushed 2d ago), licensed Apache-2.0. It adds 10,564 tokens to every session, about $0.0423 per session on Opus 5.5. A static security scan graded it A with 0 findings. It is 77% identical to obsidian-mcp-server AGENTS.md, differing in 420 lines, and is treated as a copy.
Other instructions, from other repositories
vscode buildNext.instructions.md
Working notes and architecture documentation for the new esbuild-based build system in build/next. Use when making changes to the new build pipeline (transpile/bundle commands, NLS plugin, source-map handling, resource copying, or self-hosting watch tasks).
next.js AGENTS.md
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