# Chembl (npm · @pipeworx/mcp-chembl)

ChEMBL MCP — drug discovery database (EBI).

- Trust score: 82/100 (high trust)
- Change this week: +3
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- remote · `gateway.pipeworx.io`: 63/100, [markdown](https://verifymcp.io/servers/pipeworx-io-chembl/chembl-mcp.md), [page](https://verifymcp.io/servers/pipeworx-io-chembl/chembl-mcp)
- npm · `@pipeworx/mcp-chembl`: 82/100 (this document), [markdown](https://verifymcp.io/servers/pipeworx-io-chembl/pipeworx-mcp-chembl.md), [page](https://verifymcp.io/servers/pipeworx-io-chembl/pipeworx-mcp-chembl)

## Channel facts

- Registry: `npm`
- Package: `@pipeworx/mcp-chembl`
- Version: `0.2.1`
- Transport: `stdio`

## Trust breakdown

How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. Scores are 0–100 per category. Scoring method: https://verifymcp.io/docs/scoring (what has changed: https://verifymcp.io/docs/scoring/changelog)

Scored 2026-11-05.

- **Supply Chain Security**: 100/100
  - No malware found by supply-chain analysis.
  - No known CVEs affecting this package version or its production dependencies.
  - No install/post-install scripts declared.
  - No production dependencies, so there is no dependency health to assess.
- **Provenance & Transparency**: 97/100
  - Source repository is publicly reachable at the declared URL.
  - Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-chembl).
  - Clear OSI-approved license (MIT).
  - Actively maintained (last published 5 days ago).
  - Disclosure check failed: no security disclosure policy was found in the source repository.
- **Schema Quality & AI Usability**: 67/100
  - AI-judged instruction clarity (good).
  - Context-footprint check failed: tool/resource definitions use about 982 tokens (~140/item across 7 items; 7 tools + 0 resources), over budget; trim descriptions and params.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 23/100
  - Stability observed for 7 of 30 days with no destabilising changes; credit accrues until the full window elapses.
- **Tool Coverage**: 88/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 65% of tool parameters carry a description.
- **Tool Safety**: 100/100
  - No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.
  - We read all 7 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 8 captured unit(s) of tool text and found none that tries to manipulate the model reading it.
- **Capabilities**: 100/100
  - Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.

## Install

### How do I install the Chembl MCP server?

Chembl runs locally as an npm package, launched with npx -y @pipeworx/mcp-chembl. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.

### Claude

```bash
claude mcp add pipeworx-io-chembl -- npx -y @pipeworx/mcp-chembl
```

### Cursor

```json
{
  "mcpServers": {
    "pipeworx-io-chembl": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-chembl"
      ]
    }
  }
}
```

### VS Code

```json
{
  "servers": {
    "pipeworx-io-chembl": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-chembl"
      ]
    }
  }
}
```

### Codex

```bash
codex mcp add pipeworx-io-chembl -- npx -y @pipeworx/mcp-chembl
```

### opencode

```json
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "pipeworx-io-chembl": {
      "type": "local",
      "command": [
        "npx",
        "-y",
        "@pipeworx/mcp-chembl"
      ],
      "enabled": true
    }
  }
}
```

### OpenClaw

```bash
openclaw mcp add pipeworx-io-chembl --command npx --arg -y --arg @pipeworx/mcp-chembl
```

### Hermes

```yaml
mcp_servers:
  pipeworx-io-chembl:
    command: "npx"
    args: ["-y", "@pipeworx/mcp-chembl"]
```

### Netclaw

```json
{
  "McpServers": {
    "pipeworx-io-chembl": {
      "Transport": "stdio",
      "Command": "npx",
      "Arguments": [
        "-y",
        "@pipeworx/mcp-chembl"
      ]
    }
  }
}
```

### Vellum

```bash
assistant mcp add pipeworx-io-chembl -t stdio -c npx -a -y @pipeworx/mcp-chembl
```

### Other

```json
{
  "mcpServers": {
    "pipeworx-io-chembl": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-chembl"
      ]
    }
  }
}
```

## Changelog

Every change recorded for this component, newest first. Days that predate change tracking, or that we cannot explain, say so: "we were watching and nothing happened" and "we were not watching" are different claims.

### 2026-11-05 (score 82, +1)

No change was recorded against any check on this day. Stability & Change Management went from 20 to 23. That category is still filling its 30-day observation window: 6 days of observed history at the previous scan, 7 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-11-03 (score 81, +1)

No change was recorded against any check on this day. Stability & Change Management went from 13 to 17. That category is still filling its 30-day observation window: 4 days of observed history at the previous scan, 5 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-11-01 (score 80, +16)

- [security improvement] Malware scan: unverified → pass

### 2026-10-31 (score 64, −15)

- [security regression] Malware scan: pass → unverified
- [functional] Package version: 0.2.0 → 0.2.1

### 2026-10-29 (score 79)

First indexed and scored.

## MCP tools (7)

### `search` (~118 tokens)

Full-text search the ChEMBL drug-discovery database for molecules, targets, assays, or documents; returns ChEMBL IDs and summary fields you can pass to `molecule`, `target`, or `activities`. Pair with `chembl_mechanism`, which takes a drug name directly and returns its mechanism of action and target.

Input parameters:

- `limit` (number): 1-1000 (default 25).
- `query` (string, required): Free-text query.
- `type` (string): molecule (default) | target | assay | document

### `molecule` (~37 tokens)

Full molecule record by ChEMBL ID (e.g. "CHEMBL25" = aspirin).

Input parameters:

- `chembl_id` (string, required)

### `target` (~25 tokens)

Target record by ChEMBL target ID.

Input parameters:

- `chembl_id` (string, required)

### `mechanism` (~85 tokens)

Raw ChEMBL mechanism records for one exact molecule ChEMBL ID (e.g. "CHEMBL1703"), returned verbatim from the API. Use when you already hold the precise molecule ID and want the unshaped rows; to start from a drug name, call `chembl_mechanism`.

Input parameters:

- `chembl_id` (string, required): molecule_chembl_id

### `chembl_mechanism` (~470 tokens)

Mechanism of action of a drug, from its NAME (or a ChEMBL molecule ID). Answers "how does metformin work", "what is the mechanism of action of X", "what does X inhibit", "what target does X act on", "X mode of action", "is X an agonist or an antagonist", "X molecular target". Resolves the drug name to every matching ChEMBL molecule form — the base compound together with its salts, hydrochlorides, mesylates and branded formulations — and searches all of them at once, so a drug whose pharmacology is curated on the salt form still resolves. Returns, per mechanism: action_type (INHIBITOR, AGONIST, ANTAGONIST, BLOCKER, MODULATOR, ...), the mechanism_of_action sentence (e.g. "Mitochondrial complex I (NADH dehydrogenase) inhibitor"), the molecular target with its ChEMBL target ID, target name and organism, the exact molecule form the mechanism is recorded on with its preferred name, max clinical phase, curator mechanism/selectivity comments, and PubMed references. Also lists every molecule ID searched, so an empty result is interpretable. Curated pharmacology from ChEMBL (EMBL-EBI). Reach for this for pharmacology, mode of action, drug-target identification, and any "how does this drug work" question.

Input parameters:

- `candidates` (number): How many name-matched molecule forms to search across, 1-25 (default 10). Higher catches obscure salt forms.
- `chembl_id` (string): Alias for molecule_chembl_id.
- `drug` (string): Drug name, e.g. "metformin", "imatinib", "aspirin". Brand, generic, or salt names all work.
- `limit` (number): Max mechanisms returned, 1-200 (default 50).
- `molecule_chembl_id` (string): Exact ChEMBL molecule ID instead of a name, e.g. "CHEMBL1431". Salt forms of this molecule are included automatically.
- `name` (string): Alias for drug.
- `q` (string): Alias for drug.
- `query` (string): Alias for drug.

### `activities` (~119 tokens)

Retrieve bioactivity records from ChEMBL filtered by molecule_chembl_id and/or target_chembl_id; returns IC50/Ki/EC50 values, assay descriptions, and units. This is SMALL-MOLECULE assay data: a biologic such as an antibody has none by construction, and the response says so rather than returning a bare empty list.

Input parameters:

- `limit` (number): 1-1000 (default 25).
- `molecule_chembl_id` (string)
- `target_chembl_id` (string)

### `drug_indications` (~75 tokens)

Retrieve approved drug indication records from ChEMBL filtered by molecule_chembl_id and/or MeSH disease ID; returns disease names, efo_id cross-references, and max clinical trial phase.

Input parameters:

- `limit` (number)
- `mesh_id` (string)
- `molecule_chembl_id` (string)

## Diagnostics

Captured diagnostic sections: Provenance, Dependencies. The full working is on the page: https://verifymcp.io/servers/pipeworx-io-chembl/pipeworx-mcp-chembl#diagnostics

## Score history

- 2026-11-05: 82
- 2026-11-04: 81
- 2026-11-03: 81
- 2026-11-02: 80
- 2026-11-01: 80
- 2026-10-31: 64
- 2026-10-30: 79
- 2026-10-29: 79

## Common questions

### What is the Chembl MCP server?

Chembl is an MCP server listed in the public MCP registry as io.github.pipeworx-io/chembl. ChEMBL MCP, drug discovery database (EBI). This page covers its npm package (@pipeworx/mcp-chembl).

### Is the Chembl MCP server safe to use?

Chembl scores 82 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. It declares no install or post-install scripts. Its build provenance is signed and verified. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.

### What tools does the Chembl MCP server expose?

Chembl exposes 7 tools: search, molecule, target, mechanism, chembl_mechanism, and 2 more. Their descriptions and schemas cost roughly 929 tokens of context every time the server is loaded.

### Is the Chembl MCP server still maintained?

Chembl is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.

### What licence is the Chembl MCP server under?

Chembl declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.

### What did VerifyMCP test on the Chembl MCP server?

VerifyMCP ran 16 checks on Chembl, covering Malware scan, Known CVEs, Install scripts, Dependency health and 12 more. Endpoint Security and Transport & Reachability do not apply to an npm package, so they were not tested. The score does not measure everything, and the scoring documentation lists what it leaves out.

## Links

- npm package: https://www.npmjs.com/package/@pipeworx/mcp-chembl
- Socket report: https://socket.dev/npm/package/@pipeworx/mcp-chembl
- Repository: https://github.com/pipeworx-io/mcp-chembl
- Website: https://pipeworx.io/packs/chembl
- Changelog RSS feed: https://verifymcp.io/servers/pipeworx-io-chembl/pipeworx-mcp-chembl.xml
- Changelog JSON feed: https://verifymcp.io/servers/pipeworx-io-chembl/pipeworx-mcp-chembl/changelog.json
- Trust report (JSON): https://verifymcp.io/servers/pipeworx-io-chembl/pipeworx-mcp-chembl.json
- HTML version of this page: https://verifymcp.io/servers/pipeworx-io-chembl/pipeworx-mcp-chembl