Uniprot
NPM · @PIPEWORX/MCP-UNIPROT · 2 COMPONENTS
UniProt MCP — protein sequence + function database.
Available components
Last scanned (8 hours ago)
Scores higher than 58% of npm servers
Category Health and Science
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. How we score → Why this is hard to score →
Supply Chain Security100
- No malware found by supply-chain analysis.Pass
- No known CVEs affecting this package version or its production dependencies.Pass
- No install/post-install scripts declared.Pass
- No production dependencies, so there is no dependency health to assess. View diagnostics → Pass
Provenance & Transparency97
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-uniprot). View diagnostics → Pass
- Clear OSI-approved license (MIT).Pass
- Actively maintained (last published 6 days ago).Pass
- Disclosure check failed: no security disclosure policy was found in the source repository. See how to fix → Fail
Schema Quality & AI Usability68
- AI-judged instruction clarity (good).Pass
- 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. See how to fix → Fail
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management0
- Stability not yet verified: not enough scan history yet (needs a 30-day window).Unverified
Tool Coverage83
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 50% of tool parameters carry a description.Partial
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 6 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 7 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.Pass
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.
Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 30 Oct 26 0
- Security disclosure: unverified → fail ▼ functional
- 29 Oct 26 78
First indexed and scored.
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 5 Nov 2026 · Analysed npm/@pipeworx/mcp-uniprot@0.2.0
Provenance Verified
A signed build attestation was found and verified, binding this exact artifact to the source repository it claims to come from.
| Result | Verified |
|---|---|
| Ecosystem | npm |
| Reason | Verified |
| Discovered via | Registry attestation endpoint |
| Source repo | pipeworx-io/mcp-uniprot |
| Certificate issuer | https://token.actions.githubusercontent.com |
| Certificate SAN | https://github.com/pipeworx-io/mcp-uniprot/.github/workflows/publish.yml@refs/heads/main |
| Rekor log index | 3560811494 |
| Predicate type | SLSA build provenance https://slsa.dev/provenance/v1 |
| Subject digest | sha512:be228c1e25a7df990d741b7d3b772123ad494e3bb028e2a27c1ab81c0defc3baedccee1f915aaee997f2ace478e474a7224ce7625f2d161029d74d7c8 |
Background: How many MCP packages publish verified provenance →
Dependencies 0 packages
| Packages resolved | 0 |
|---|---|
| Tree resolution | Complete |
Background: SBOMs and build attestations, explained →
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
feature_summary ~94
"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.
| Name | Type | Req | Description |
|---|---|---|---|
| accession | string | yes | – |
No output schema declared.
No examples provided.
get ~142
"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.
| Name | Type | Req | Description |
|---|---|---|---|
| accession | string | yes | e.g. "P12345" or "P38398" (BRCA1_HUMAN) |
| format | string | – | json (default) | fasta | xml | txt | gff |
No output schema declared.
No examples provided.
keyword ~66
"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".
| Name | Type | Req | Description |
|---|---|---|---|
| keyword_id | string | yes | – |
No output schema declared.
No examples provided.
proteomes_search ~68
"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.
| Name | Type | Req | Description |
|---|---|---|---|
| query | string | yes | – |
| size | number | – | – |
No output schema declared.
No examples provided.
search ~244
"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.
| Name | Type | Req | Description |
|---|---|---|---|
| fields | string | – | Comma-sep returned fields (json/tsv only). |
| format | string | – | json (default) | tsv | fasta | xml |
| query | string | yes | 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) |
No output schema declared.
No examples provided.
taxonomy_search ~106
"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).
| Name | Type | Req | Description |
|---|---|---|---|
| query | string | yes | – |
| size | number | – | – |
No output schema declared.
No examples provided.
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.
npm · @pipeworx/mcp-uniprot
claude mcp add pipeworx-io-uniprot -- npx -y @pipeworx/mcp-uniprot
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.