io.github.cyanheads/chembl-mcp-server

io.github.cyanheads/chembl-mcp-serverv0.5.0Other

Link compounds to protein targets, rank bioactivity, and look up drug mechanisms and indications.

The current version, v0.5.0, was published to the official MCP registry on 2026-10-29. It is distributed as @cyanheads/chembl-mcp-server on npm and as a hosted remote over streamable-http, filed under Other by this index, and declares 15 environment variables. Removals and unreachable sources are measured across every server this index tracks, contract drift across the servers that answer in consecutive snapshots; the index's current counts put this record in context.

In-path gate · all MCP tools

Using io.github.cyanheads/chembl-mcp-server in Claude, Cursor, Gemini CLI, Cline, or Zed?

MCP tool contracts can change remotely with no version bump. The mcpindex gate pins each contract and HOLDs the call when it drifts-before your agent acts. Zero credentials. This is not the package install for this server itself (use Install this server for that).

Install the mcpindex gate (one command)

Rewrites your MCP host config so each server launches behind the gate. Inspect first: curl -fsSL https://mcpindex.ai/install.sh | less

uv tool install mcpindex-gate && mcpindex-config-wire

Auditable install path →Watch it hold a drift →

Trust verdict · v1 advisory · method

REVIEWstatus: PARTIALfresh until 2026-11-18 01:58 UTC

screened 2026-10-16tier: scannedgranularity: description-levelsource: registry

Semantic screen found no manipulation pattern in the description. Conformance probe not yet run.

mcpindex.integrity.descriptionpassINFO

evidence“Tool links compounds to protein targets and ranks bioactivity.”via static_description

Limits of this verdict

- Semantic screen only - the deterministic conformance probe has not run on this server
- Confidence is reported but not yet calibrated (v1)
- Screen reads the tool description, not the live behavior
- advisory
- registry description only no input schema
- screen model 8b
- Still current: the description we screened is unchanged, re-checked against the registry
- The registry listing (version, packages, links) changed after this screen ran - the description we assessed did not

Semantic screen: an LLM judge reads the tool description for hidden instructions (status PARTIAL). A pass means the description is not lying, not that the tool is safe: a high-capability tool with an honest description still warrants caution. The deterministic conformance probe has not been run on this server yet, so the screen here is semantic-only. Posture: advisory. Confidences are reported but not yet calibrated (calibrated=false at v1). Full verdict history is not shown on this page.

Own this server? Test a description on the public screen → It is a separate check from the verdict above, so the two can differ.

That verdict was true at screening time (snapshot 2026-11-11).

Contracts can change after screening, with no version bump. The gate pins io.github.cyanheads/chembl-mcp-server’s tool contracts on first sight and holds any silent change before your agent acts - the check that keeps being true on Tuesday.

See your first HOLD in 2 minutes →

Contract drift · crawler-observed · ledger

7 contract changes observedmost recent Thu, 29 Oct 2026 14:00:00 GMTsafety-relevant diff

7 changes with a version change.

what changednew optional inputinput constraint tightenedoutput shape changed

injected context changedmost recent Sun, 25 Oct 2026 04:00:00 GMTsafety-relevant diff

what changedinjected server instructions changed

Server-scoped, not a tool: this is text the server supplies for clients to inject into an agent’s context on connect (instructions or prompt metadata). It sits outside every tool contract hash, so this observation is its only drift signal.

Part of a publisher-wide change of the same kind on 2026-10-29, seen on 20 servers from this publisher.

Part of a publisher-wide change to server context of the same kind on 2026-10-25, seen on 10 servers from this publisher.

Part of a publisher-wide change of the same kind on 2026-10-25, seen on 19 servers from this publisher.

Part of a publisher-wide change to server context of the same kind on 2026-10-19, seen on 10 servers from this publisher.

Part of a publisher-wide change of the same kind on 2026-10-19, seen on 13 servers from this publisher.

Part of a publisher-wide change of the same kind on 2026-09-20, seen on 13 servers from this publisher.

Part of a publisher-wide change of the same kind on 2026-08-26, seen on 32 servers from this publisher.

Observed by mcpindex’s crawler between daily registry snapshots - a contract diff, not a safety verdict, and not an in-path prevention (that is the gate). A “safety-relevant diff” touches a safety-relevant field; it is not a confirmed vulnerability. Shown at the server level; individual tools are not named. Absence is not a clean bill of health: only public-registry servers are crawled.

Cite this record

People vet a server before wiring it in. One line on your project site or docs answers that with an independent record: screening verdict, registry provenance, contract drift history. It stays current as new screens and drift events land.

Markdown

[Independent trust record for io.github.cyanheads/chembl-mcp-server](https://mcpindex.ai/server/io-github-cyanheads-chembl-mcp-server) - screening verdict, registry provenance, and contract drift monitoring.

HTML

<a href="https://mcpindex.ai/server/io-github-cyanheads-chembl-mcp-server">Independent trust record for io.github.cyanheads/chembl-mcp-server</a> - screening verdict, registry provenance, and contract drift monitoring.

Embed this badge

A live verdict badge for your README or listing. It reflects the current screen, links back here, and updates when the verdict does.

Markdown

[![mcpindex](https://mcpindex.ai/api/v1/badge/io-github-cyanheads-chembl-mcp-server)](https://mcpindex.ai/server/io-github-cyanheads-chembl-mcp-server)

HTML

<a href="https://mcpindex.ai/server/io-github-cyanheads-chembl-mcp-server"><img src="https://mcpindex.ai/api/v1/badge/io-github-cyanheads-chembl-mcp-server" alt="mcpindex verdict" height="20" /></a>

Environment variables

CANVAS_PROVIDER_TYPE

DataCanvas provider for the bioactivity spill and the chembl_dataframe_* SQL tools; DuckDB is the default. Set to 'none' to disable it: large bioactivity sets then inline a preview but never spill.

CHEMBL_API_BASE_URL

Base URL for the ChEMBL REST data API. Override for a private mirror or pinned host.

CHEMBL_REQUEST_TIMEOUT_MS

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).

CHEMBL_MAX_PAGE_SIZE

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.

CHEMBL_DEFAULT_LIMIT

Default result limit applied when callers omit it.

CHEMBL_MAX_SPILL_ROWS

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".

CHEMBL_MAX_CONCURRENT_PAGES

Most chembl_get_bioactivities spill-page requests in flight at once (1–6), shared by every call on the server.

CHEMBL_SPILL_DEADLINE_MS

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".

CHEMBL_DATAFRAME_DROP_ENABLED

Set to 'true' to register the opt-in chembl_dataframe_drop tool (absent from tools/list when off).

MCP_LOG_LEVEL

Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').

MCP_TRANSPORT_TYPE

Selects the HTTP transport.

MCP_HTTP_HOST

The hostname for the HTTP server.

MCP_HTTP_PORT

The port to run the HTTP server on.

MCP_HTTP_ENDPOINT_PATH

The endpoint path for the MCP server.

MCP_AUTH_MODE

Authentication mode to use: 'none', 'jwt', or 'oauth'.

MCP_LOG_LEVEL

Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').

CANVAS_PROVIDER_TYPE

DataCanvas provider for the bioactivity spill and the chembl_dataframe_* SQL tools; DuckDB is the default. Set to 'none' to disable it: large bioactivity sets then inline a preview but never spill.

CHEMBL_API_BASE_URL

Base URL for the ChEMBL REST data API. Override for a private mirror or pinned host.

CHEMBL_REQUEST_TIMEOUT_MS

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).

CHEMBL_MAX_PAGE_SIZE

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.

CHEMBL_DEFAULT_LIMIT

Default result limit applied when callers omit it.

CHEMBL_MAX_SPILL_ROWS

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".

CHEMBL_MAX_CONCURRENT_PAGES

Most chembl_get_bioactivities spill-page requests in flight at once (1–6), shared by every call on the server.

CHEMBL_SPILL_DEADLINE_MS

CHEMBL_DATAFRAME_DROP_ENABLED

Set to 'true' to register the opt-in chembl_dataframe_drop tool (absent from tools/list when off).

MCP quality score · maturity, not trust · methodology

freshness

completeness

installability

documentation

stability

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Install this server

Remote endpoint

Streamable HTTP / SSE endpoint. Add to any MCP client that supports remote servers.

https://chembl.caseyjhand.com/mcp

Claude Desktop (claude_desktop_config.json)

{
  "mcpServers": {
    "chembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "--",
        "@cyanheads/chembl-mcp-server"
      ],
      "env": {
        "CANVAS_PROVIDER_TYPE": "duckdb",
        "CHEMBL_API_BASE_URL": "https://www.ebi.ac.uk/chembl/api/data",
        "CHEMBL_REQUEST_TIMEOUT_MS": "30000",
        "CHEMBL_MAX_PAGE_SIZE": "1000",
        "CHEMBL_DEFAULT_LIMIT": "25",
        "CHEMBL_MAX_SPILL_ROWS": "50000",
        "CHEMBL_MAX_CONCURRENT_PAGES": "4",
        "CHEMBL_SPILL_DEADLINE_MS": "45000",
        "CHEMBL_DATAFRAME_DROP_ENABLED": "false",
        "MCP_LOG_LEVEL": "info",
        "MCP_TRANSPORT_TYPE": "<mcp_transport_type>",
        "MCP_HTTP_HOST": "127.0.0.1",
        "MCP_HTTP_PORT": "3010",
        "MCP_HTTP_ENDPOINT_PATH": "/mcp",
        "MCP_AUTH_MODE": "none"
      }
    }
  }
}

Cursor (.cursor/mcp.json)

{
  "mcpServers": {
    "chembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "--",
        "@cyanheads/chembl-mcp-server"
      ],
      "env": {
        "CANVAS_PROVIDER_TYPE": "duckdb",
        "CHEMBL_API_BASE_URL": "https://www.ebi.ac.uk/chembl/api/data",
        "CHEMBL_REQUEST_TIMEOUT_MS": "30000",
        "CHEMBL_MAX_PAGE_SIZE": "1000",
        "CHEMBL_DEFAULT_LIMIT": "25",
        "CHEMBL_MAX_SPILL_ROWS": "50000",
        "CHEMBL_MAX_CONCURRENT_PAGES": "4",
        "CHEMBL_SPILL_DEADLINE_MS": "45000",
        "CHEMBL_DATAFRAME_DROP_ENABLED": "false",
        "MCP_LOG_LEVEL": "info",
        "MCP_TRANSPORT_TYPE": "<mcp_transport_type>",
        "MCP_HTTP_HOST": "127.0.0.1",
        "MCP_HTTP_PORT": "3010",
        "MCP_HTTP_ENDPOINT_PATH": "/mcp",
        "MCP_AUTH_MODE": "none"
      }
    }
  }
}

Cline (cline_mcp_settings.json)

{
  "mcpServers": {
    "chembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "--",
        "@cyanheads/chembl-mcp-server"
      ],
      "env": {
        "CANVAS_PROVIDER_TYPE": "duckdb",
        "CHEMBL_API_BASE_URL": "https://www.ebi.ac.uk/chembl/api/data",
        "CHEMBL_REQUEST_TIMEOUT_MS": "30000",
        "CHEMBL_MAX_PAGE_SIZE": "1000",
        "CHEMBL_DEFAULT_LIMIT": "25",
        "CHEMBL_MAX_SPILL_ROWS": "50000",
        "CHEMBL_MAX_CONCURRENT_PAGES": "4",
        "CHEMBL_SPILL_DEADLINE_MS": "45000",
        "CHEMBL_DATAFRAME_DROP_ENABLED": "false",
        "MCP_LOG_LEVEL": "info",
        "MCP_TRANSPORT_TYPE": "<mcp_transport_type>",
        "MCP_HTTP_HOST": "127.0.0.1",
        "MCP_HTTP_PORT": "3010",
        "MCP_HTTP_ENDPOINT_PATH": "/mcp",
        "MCP_AUTH_MODE": "none"
      }
    }
  }
}

Zed (~/.config/zed/settings.json)

Merge into the context_servers block of your Zed settings.

{
  "context_servers": {
    "chembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "--",
        "@cyanheads/chembl-mcp-server"
      ],
      "env": {
        "CANVAS_PROVIDER_TYPE": "duckdb",
        "CHEMBL_API_BASE_URL": "https://www.ebi.ac.uk/chembl/api/data",
        "CHEMBL_REQUEST_TIMEOUT_MS": "30000",
        "CHEMBL_MAX_PAGE_SIZE": "1000",
        "CHEMBL_DEFAULT_LIMIT": "25",
        "CHEMBL_MAX_SPILL_ROWS": "50000",
        "CHEMBL_MAX_CONCURRENT_PAGES": "4",
        "CHEMBL_SPILL_DEADLINE_MS": "45000",
        "CHEMBL_DATAFRAME_DROP_ENABLED": "false",
        "MCP_LOG_LEVEL": "info",
        "MCP_TRANSPORT_TYPE": "<mcp_transport_type>",
        "MCP_HTTP_HOST": "127.0.0.1",
        "MCP_HTTP_PORT": "3010",
        "MCP_HTTP_ENDPOINT_PATH": "/mcp",
        "MCP_AUTH_MODE": "none"
      }
    }
  }
}

Claude Code (claude mcp add)

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

Gemini CLI (gemini mcp add)

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

Verdict API

curl -s mcpindex.ai/api/v1/trust/server/io-github-cyanheads-chembl-mcp-server

Free-tier verdict as JSON: decision + dimensions + severity. Call it from your agent before it invokes a tool it just discovered.

Details

version: v0.5.0
category: Other
verdict expires: 2026-11-18
quality: 80 / 100
operator: cyanheads

Listing

Listed from the official MCP registry. Unclaimed by its maintainer. Maintainer? Verify it → · or email us →

Provenance

Each verdict is bound to a hash of the exact description it judged, so a re-crawl that changes the text produces a new record rather than silently inheriting this one. Verdict history is hash-chained and anchored to Bitcoin via OpenTimestamps (latest confirmed at block 975,257). Verify it yourself.

Links

Repository →

Remote endpoint

https://chembl.caseyjhand.com/mcp