# Bindingdb (npm · @pipeworx/mcp-bindingdb)

BindingDB — measured protein/small-molecule binding affinities.

- Trust score: 83/100 (high trust)
- Change this week: +3
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- remote · `gateway.pipeworx.io`: 77/100, [markdown](https://verifymcp.io/servers/pipeworx-io-bindingdb/bindingdb-mcp.md), [page](https://verifymcp.io/servers/pipeworx-io-bindingdb/bindingdb-mcp)
- npm · `@pipeworx/mcp-bindingdb`: 83/100 (this document), [markdown](https://verifymcp.io/servers/pipeworx-io-bindingdb/pipeworx-mcp-bindingdb.md), [page](https://verifymcp.io/servers/pipeworx-io-bindingdb/pipeworx-mcp-bindingdb)

## Channel facts

- Registry: `npm`
- Package: `@pipeworx/mcp-bindingdb`
- 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-bindingdb).
  - 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**: 68/100
  - AI-judged instruction clarity (good).
  - Context-footprint check failed: tool/resource definitions use about 559 tokens (~186/item across 3 items; 3 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**: 100/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 100% 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 3 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 4 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 Bindingdb MCP server?

Bindingdb runs locally as an npm package, launched with npx -y @pipeworx/mcp-bindingdb. 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-bindingdb -- npx -y @pipeworx/mcp-bindingdb
```

### Cursor

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

### VS Code

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

### Codex

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

### opencode

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

### OpenClaw

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

### Hermes

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

### Netclaw

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

### Vellum

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

### Other

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

## 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 83, +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 82, +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.

### 2026-10-31 (score 81, +16)

- [security improvement] Malware scan: unverified → pass

### 2026-10-30 (score 65, −15)

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

### 2026-10-29 (score 80)

First indexed and scored.

## MCP tools (3)

### `bindingdb_ligands_by_uniprot` (~221 tokens)

Measured binding affinities (Ki, Kd, IC50, EC50 in nM) for every ligand BindingDB has curated against a UniProt target, each with the PubMed ID of the paper it was measured in. AUTHORITATIVE for "what compounds bind this protein and how tightly" — this is experimental medicinal-chemistry data, not a prediction or a web summary. Pass one or more UniProt accessions (e.g. P24941 for CDK2).

Input parameters:

- `cutoff` (number): Affinity cutoff in nM — only measurements at or below this are returned. Default 10. Raising it enlarges the upstream response substantially (100 nM on a well-studied kinase is several MB).
- `limit` (number): Max rows to return, 1-500 (default 50). Sorted by potency.
- `uniprot` (string, required): UniProt accession, or several comma-separated (e.g. "P24941" or "P24941,P00533")

### `bindingdb_targets_by_smiles` (~163 tokens)

Given a compound SMILES, the protein targets BindingDB has measured it (or a structurally similar compound) against, with species and affinity. AUTHORITATIVE for compound-to-target and off-target lookups grounded in published measurements. Use a similarity cutoff below 1.0 to pull analogues as well as the exact structure.

Input parameters:

- `limit` (number): Max rows to return, 1-500 (default 50)
- `similarity` (number): Tanimoto similarity cutoff 0-1 (default 0.85). 1.0 means exact structure only.
- `smiles` (string, required): Compound SMILES (e.g. "CC(=O)Oc1ccccc1C(=O)O" for aspirin)

### `bindingdb_by_pdb` (~123 tokens)

Measured binding affinities for the ligands associated with a PDB structure entry, linking a solved co-crystal to the potency numbers published for that target. AUTHORITATIVE for "what is the measured affinity of the ligand in this PDB structure". Takes a single 4-character PDB ID (e.g. 3EML).

Input parameters:

- `limit` (number): Max rows to return, 1-500 (default 50)
- `pdb` (string, required): PDB entry ID, 4 characters (e.g. "3EML")

## Diagnostics

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

## Score history

- 2026-11-05: 83
- 2026-11-04: 82
- 2026-11-03: 82
- 2026-11-02: 81
- 2026-11-01: 81
- 2026-10-31: 81
- 2026-10-30: 65
- 2026-10-29: 80

## Common questions

### What is the Bindingdb MCP server?

Bindingdb is an MCP server listed in the public MCP registry as io.github.pipeworx-io/bindingdb. BindingDB, measured protein/small-molecule binding affinities. This page covers its npm package (@pipeworx/mcp-bindingdb).

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

Bindingdb scores 83 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 Bindingdb MCP server expose?

Bindingdb exposes 3 tools: bindingdb_ligands_by_uniprot, bindingdb_targets_by_smiles, bindingdb_by_pdb. Their descriptions and schemas cost roughly 507 tokens of context every time the server is loaded.

### Is the Bindingdb MCP server still maintained?

Bindingdb 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 Bindingdb MCP server under?

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

## Links

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