# Uniprot (npm · @pipeworx/mcp-uniprot)

UniProt MCP — protein sequence + function database.

- Trust score: 78/100 (medium)
- Change this week: 0
- 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-uniprot/uniprot-mcp.md), [page](https://verifymcp.io/servers/pipeworx-io-uniprot/uniprot-mcp)
- npm · `@pipeworx/mcp-uniprot`: 78/100 (this document), [markdown](https://verifymcp.io/servers/pipeworx-io-uniprot/pipeworx-mcp-uniprot.md), [page](https://verifymcp.io/servers/pipeworx-io-uniprot/pipeworx-mcp-uniprot)

## Channel facts

- Registry: `npm`
- Package: `@pipeworx/mcp-uniprot`
- Version: `0.2.0`
- 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-uniprot).
  - Clear OSI-approved license (MIT).
  - Actively maintained (last published 6 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 774 tokens (~129/item across 6 items; 6 tools + 0 resources), over budget; trim descriptions and params.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 0/100
  - Stability not yet verified: not enough scan history yet (needs a 30-day window).
- **Tool Coverage**: 83/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 50% 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 6 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 7 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.

**Unverified: 1 category.** A category scored 0 because we could not verify it: a data source with nothing on this package, evidence we could not reach, or a check we could not run. We only credit what we can confirm.

## Install

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

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

### Cursor

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

### VS Code

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

### Codex

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

### opencode

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

### OpenClaw

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

### Hermes

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

### Netclaw

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

### Vellum

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

### Other

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

## 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.

### 2026-10-30 (score 78, 0)

- [functional regression] Security disclosure: unverified → fail

### 2026-10-29 (score 78)

First indexed and scored.

## MCP tools (6)

### `search` (~244 tokens)

"Find protein [name]" / "look up [gene] in UniProt" / "BRCA1 / TP53 / insulin protein info" / "all proteins for [organism]" — UniProtKB search via Lucene-style queries (e.g. gene:BRCA1 AND organism_id:9606 for human BRCA1). UniProt is the authoritative protein-sequence-and-function database — use for protein characterization, function annotation, sequence retrieval, and cross-references to PDB/GO/PubMed.

Input parameters:

- `fields` (string): Comma-sep returned fields (json/tsv only).
- `format` (string): json (default) | tsv | fasta | xml
- `query` (string, required): Lucene-style expression, passed bare — do NOT wrap the whole thing in quotes. Fielded terms combine with AND, e.g. gene:BRCA1 AND organism_id:9606. Quotes are only for a multi-word value, e.g. organi…
- `size` (number): 1-500 (default 25)

### `get` (~142 tokens)

"Fetch protein [P12345]" / "UniProt entry for [accession]" / "FASTA sequence for [protein]" — single UniProtKB entry by accession (e.g. P12345 or P38398 for BRCA1_HUMAN). Returns full protein record: sequence, function annotations, GO terms, cross-refs, post-translational modifications, variants. Pass format=fasta for sequence only.

Input parameters:

- `accession` (string, required): e.g. "P12345" or "P38398" (BRCA1_HUMAN)
- `format` (string): json (default) | fasta | xml | txt | gff

### `proteomes_search` (~68 tokens)

"Reference proteome for [organism]" / "complete protein set of [species]" — search UniProt reference proteomes (the curated representative protein set per organism). Use as a starting point for genome-scale protein analyses.

Input parameters:

- `query` (string, required)
- `size` (number)

### `taxonomy_search` (~106 tokens)

"NCBI taxonomy ID for [organism]" / "taxid for [species]" / "look up [Latin name] in NCBI taxonomy" — search NCBI Taxonomy via UniProt's mirror. Returns taxonomic IDs you can use as organism_id filters in `search` (9606 = human, 10090 = mouse, 7227 = D. melanogaster, etc).

Input parameters:

- `query` (string, required)
- `size` (number)

### `keyword` (~66 tokens)

"UniProt keyword KW-N info" / "what does keyword [X] mean" — fetch a UniProt controlled-vocabulary keyword by ID. Use to look up annotation tags like "Kinase" / "Membrane" / "Disease-associated".

Input parameters:

- `keyword_id` (string, required)

### `feature_summary` (~94 tokens)

"Domain map of [protein]" / "annotated features of [accession]" / "what regions / sites does [protein] have" — annotated features (domains, active sites, transmembrane regions, mutagenesis sites, glycosylation, disulfide bonds, etc.) for a UniProt accession. Use for structural/functional analysis without pulling the full protein record.

Input parameters:

- `accession` (string, required)

## Diagnostics

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

## Score history

- 2026-11-05: 78
- 2026-11-04: 78
- 2026-11-03: 78
- 2026-11-02: 78
- 2026-11-01: 78
- 2026-10-31: 78
- 2026-10-30: 78
- 2026-10-29: 78

## Common questions

### What is the Uniprot MCP server?

Uniprot is an MCP server listed in the public MCP registry as io.github.pipeworx-io/uniprot. UniProt MCP, protein sequence + function database. This page covers its npm package (@pipeworx/mcp-uniprot).

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

Uniprot scores 78 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 Uniprot MCP server expose?

Uniprot exposes 6 tools: search, get, proteomes_search, taxonomy_search, keyword, feature_summary. Their descriptions and schemas cost roughly 720 tokens of context every time the server is loaded.

### Is the Uniprot MCP server still maintained?

Uniprot 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 Uniprot MCP server under?

Uniprot 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 Uniprot MCP server?

VerifyMCP ran 15 checks on Uniprot, covering Malware scan, Known CVEs, Install scripts, Dependency health and 11 more. One item could not be completed, a gap on our side rather than a finding about Uniprot: Stability. One category scores 0 for that reason, because we only credit what we can confirm. 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-uniprot
- Socket report: https://socket.dev/npm/package/@pipeworx/mcp-uniprot
- Repository: https://github.com/pipeworx-io/mcp-uniprot
- Website: https://pipeworx.io/packs/uniprot
- Changelog RSS feed: https://verifymcp.io/servers/pipeworx-io-uniprot/pipeworx-mcp-uniprot.xml
- Changelog JSON feed: https://verifymcp.io/servers/pipeworx-io-uniprot/pipeworx-mcp-uniprot/changelog.json
- Trust report (JSON): https://verifymcp.io/servers/pipeworx-io-uniprot/pipeworx-mcp-uniprot.json
- HTML version of this page: https://verifymcp.io/servers/pipeworx-io-uniprot/pipeworx-mcp-uniprot