chembl-mcp-server

Name: chembl-mcp-server
Author: cyanheads

Community

MCP server by cyanheads · updated 5 days ago · ★ 1 · 310 downloads a week

Score 78

Link compounds to protein targets, rank bioactivity, and look up drug mechanisms and indications. chembl-mcp-server is a community project by cyanheads, not verified by a company domain.

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Works withClaude Code Claude Desktop Cursor Codex Gemini CLI VS Code Windsurf Antigravity CLI

Maintenance

Last commit 5 days ago

Licence

Apache-2.0: permissive, fine for commercial use

Quality

Clear description, published package or server URL, original repository

Security

No risky patterns in the files we checked

What you need

Setting	Needed	What it is
`CANVAS_PROVIDER_TYPE`Environment variable	Optional	Set to 'duckdb' to enable the bioactivity DataCanvas spill and the chembl_dataframe_* SQL tools. When 'none', large bioactivity sets inline a preview but never spill. Default: `none`
`CHEMBL_API_BASE_URL`Environment variable	Optional	Base URL for the ChEMBL REST data API. Override for a private mirror or pinned host. Default: `https://www.ebi.ac.uk/chembl/api/data`
`CHEMBL_REQUEST_TIMEOUT_MS`Environment variable	Optional	Per-attempt timeout in milliseconds for an upstream ChEMBL request, capped by what is left of the call's time budget (45 s for most calls, CHEMBL_SPILL_DEADLINE_MS for a bioactivity spill). Default: `30000`
`CHEMBL_MAX_PAGE_SIZE`Environment variable	Optional	Rows per upstream ChEMBL page (max 1000). The bioactivity spill walks pages of this size; an inline bioactivity page requests its limit, capped at this size. Default: `1000`
`CHEMBL_DEFAULT_LIMIT`Environment variable	Optional	Default result limit applied when callers omit it. Default: `25`
`CHEMBL_MAX_SPILL_ROWS`Environment variable	Optional	Ceiling on rows chembl_get_bioactivities stages to a DataCanvas table, and so on the upstream page walk behind it. Over the cap the response reports truncated: true and truncated_by: "row_cap". Default: `50000`
`CHEMBL_MAX_CONCURRENT_PAGES`Environment variable	Optional	Most chembl_get_bioactivities spill-page requests in flight at once (1–6), shared by every call on the server. Default: `4`
`CHEMBL_SPILL_DEADLINE_MS`Environment variable	Optional	Time budget in milliseconds for one chembl_get_bioactivities spill, its count and page walk (10000–600000). At expiry the rows fetched so far stage with truncated: true and truncated_by: "time_budget". Default: `45000`
`CHEMBL_DATAFRAME_DROP_ENABLED`Environment variable	Optional	Set to 'true' to register the opt-in chembl_dataframe_drop tool (absent from tools/list when off). Default: `false`
`MCP_LOG_LEVEL`Environment variable	Optional	Sets the minimum log level for output (e.g., 'debug', 'info', 'warn'). Default: `info`

From the publisher's entry in the official MCP Registry. Required settings are already in the install config below as placeholders.

Install chembl-mcp-server

Built from the published package, never by AI

claude mcp add chembl-mcp-server -- npx -y @cyanheads/chembl-mcp-server

Run in your terminal. Add --scope user to use it in every project.

Step-by-step: install chembl-mcp-server in Claude Code

{
  "mcpServers": {
    "chembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/chembl-mcp-server"
      ]
    }
  }
}

Settings, Developer, Edit config. Paste into claude_desktop_config.json and restart.

Step-by-step: install chembl-mcp-server in Claude Desktop

{
  "mcpServers": {
    "chembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/chembl-mcp-server"
      ]
    }
  }
}

Add to ~/.cursor/mcp.json (all projects) or .cursor/mcp.json (this project).

Step-by-step: install chembl-mcp-server in Cursor

{
  "servers": {
    "chembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/chembl-mcp-server"
      ]
    }
  }
}

Add to .vscode/mcp.json. VS Code uses "servers", not "mcpServers".

Step-by-step: install chembl-mcp-server in VS Code

codex mcp add chembl-mcp-server -- npx -y @cyanheads/chembl-mcp-server

Step-by-step: install chembl-mcp-server in Codex

{
  "mcpServers": {
    "chembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/chembl-mcp-server"
      ]
    }
  }
}

Add to ~/.gemini/config/mcp_config.json (all projects) or .agents/mcp_config.json (this project).

Step-by-step: install chembl-mcp-server in Antigravity CLI

gemini mcp add chembl-mcp-server npx -y @cyanheads/chembl-mcp-server

Gemini CLI was replaced by Antigravity CLI in June 2026 and remains only for enterprise licences and paid API keys.

Step-by-step: install chembl-mcp-server in Gemini CLI

MCP servers run with your permissions and can read what you give them access to. Some need an API key: check the README and add it under env in the chembl-mcp-server block.

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Security check

No download-and-run commands, hidden instructions or signs of sending keys out were found.

Checked automatically: README.md, package.json. This looks for known risky patterns and is not a full audit. How grades work

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chembl-mcp-server: common questions

How do I install chembl-mcp-server?

In Claude Code run claude mcp add chembl-mcp-server -- npx -y @cyanheads/chembl-mcp-server. For Claude Desktop, Cursor and VS Code, paste the config shown above and restart. See the install guides.

Is chembl-mcp-server the official server?

chembl-mcp-server is a community project by cyanheads, not verified by a company domain.

Is chembl-mcp-server free?

The code is published under the Apache-2.0 licence. The service it connects to may have its own pricing.

Is chembl-mcp-server safe to use?

It scores 78 of 100. Grades: maintenance A, licence A, quality C. Security check: grade A, no risky patterns found in the files checked. Review the code before you install. How grades work.

What are alternatives to chembl-mcp-server?

Similar MCP servers: Jay Code, Apple Health, codescene-mcp-server, Jacobian.

Does chembl-mcp-server work with ChatGPT?

Yes. Add its server URL in ChatGPT as a custom connector. See MCP in ChatGPT.