Uniprot MCP

Produce verifiable, release-aware protein evidence packages from UniProt and linked scientific sources. Its 40 documented tools cover uniprot, resolve, features, subcellular. It runs locally over stdio via the published package.

People connecting database tools to Claude, Cursor, VS Code, or another MCP client. The project is written in Python.

VERIFIED ACTIVE

LAST COMMIT 2026-08-24 · ★ 3 · #53 OF 151 MAINTAINED DATABASE · VERIFIED 2026-08-25

Apache-2.0 · Python servers · how we verify → /methodology

01 · Install Uniprot MCP

before you install - you'll need

Set UNIPROT_MCP_CACHE_DIR, UNIPROT_PIN_RELEASE before connecting.

Claude Code

claude mcp add smaniches-uniprot-mcp -- uvx uniprot-mcp-server

Claude Desktop / Cursor / VS Code - add to config

{
  "mcpServers": {
    "smaniches-uniprot-mcp": {
      "command": "uvx",
      "args": [
        "uniprot-mcp-server"
      ]
    }
  }
}

Same JSON for Cursor. For VS Code, rename the top-level key from `mcpServers` to `servers`.

Using another client? Same JSON, different key

Claude Desktop · mcpServers

Cursor · mcpServers

VS Code · servers

Windsurf · mcpServers

Zed · context_servers

Cline · mcpServers

Roo Code · mcpServers

Continue · mcpServers

LibreChat · mcpServers

Gemini CLI · mcpServers

Codex CLI · mcp_servers

Full setup guides: every client.

02 · Evidence

Security posture

What to check before giving this server access to your agent - from the registry, GitHub, and our own probes. We don't score safety; we show what's verifiable.

runs as local process (stdio) - runs on your machine with your user's permissions

license Apache-2.0 - declared in the repository

pypi package uniprot-mcp-server - check the name against the project README before installing (PyPI has no namespace ownership)

registry namespace io.github.smaniches is GitHub-verified and matches the repo owner

03 · What Uniprot MCP can do

Prose above is summarized from the project's README and registry record - no invented capabilities.

What you can build

With this server connected, an agent can filter by organism / type / completeness, and index search across UniProt citations.

The 40 tools it gives your agent

Extracted from the project's README - what uniprot-mcp lets an agent do.

uniprot_get_entry: - Full UniProt entry (e.g. P04637 for p53). Function, gene, organism, disease, cross-refs.
uniprot_search: - UniProt query language - gene, organism, taxon ID, reviewed flag, free text.
uniprot_get_sequence: - FASTA. PIR-style provenance comment block above the first record (BLAST+ / biopython compatible).
uniprot_get_features: - Domains, binding sites, PTMs, signal peptides - optional type filter.
uniprot_get_variants: - Natural variants and disease mutations.
uniprot_get_go_terms: - GO annotations grouped by aspect (F / P / C).
uniprot_get_cross_refs: - Raw cross-references to PDB, Pfam, Ensembl, Reactome, KEGG, STRING …
uniprot_id_mapping: - Map IDs between databases (Gene_Name → UniProtKB, PDB → UniProtKB, …).
uniprot_batch_entries: - Up to 100 entries in one call; invalid accessions filtered client-side.
uniprot_taxonomy_search: - Search UniProt taxonomy by organism name.
uniprot_get_keyword: - Keyword by ID (e.g. KW-0007 = Acetylation). Definition, synonyms, GO refs, hierarchy.
uniprot_search_keywords: - Free-text keyword search.

show all 40 tools

uniprot_get_subcellular_location: - Subcellular-location term by ID (e.g. SL-0039 = Cell membrane).
uniprot_search_subcellular_locations: - Free-text location search.
uniprot_get_uniref: - UniRef cluster by ID (UniRef50_P04637, UniRef90_P04637, UniRef100_P04637).
uniprot_search_uniref: - Cluster search with identity_tier filter (50 / 90 / 100).
uniprot_get_uniparc: - Sequence-archive record by UPI (UPI000002ED67).
uniprot_search_uniparc: - UniParc full-text search.
uniprot_get_proteome: - Proteome by UP ID (UP000005640 = human). Counts, BUSCO score, components.
uniprot_search_proteomes: - Filter by organism / type / completeness.
uniprot_get_citation: - Citation record by ID (typically a PubMed numeric ID).
uniprot_search_citations: - Index search across UniProt citations.
uniprot_resolve_pdb: - PDB structures: id + method + resolution + chain coverage.
uniprot_resolve_alphafold: - AlphaFold model id + EBI viewer URL (model id only - for pLDDT call the dedicated tool below).
uniprot_resolve_interpro: - InterPro signatures: id + entry name.
uniprot_resolve_chembl: - ChEMBL drug-target id + EBI target-card URL.
uniprot_compute_properties: - Derived sequence chemistry from the FASTA: MW / pI / GRAVY / aromaticity / charge / ε₂₈₀.
uniprot_features_at_position: - Every feature overlapping a residue position. Critical for variant-effect interpretation.
uniprot_lookup_variant: - HGVS-shorthand match (R175H, V600E, R248) against UniProt's natural-variant features.
uniprot_get_disease_associations: - Structured disease records from DISEASE-type comments: name + acronym + UniProt disease ID + OMIM cross-ref + description.
uniprot_get_active_sites: - Catalytic and ligand-binding residues: active sites, binding sites, sites, metal binding, DNA binding. The residue-level chemistry of the protein.
uniprot_get_processing_features: - Maturation features: signal peptide, propeptide, transit peptide, initiator methionine, chain, peptide. Essential for therapeutic-protein engineering and pathog
uniprot_get_ptms: - Post-translational modifications: modified residues (phospho/acetyl/methyl), glycosylation, lipidation (GPI/prenyl/palmitoyl), disulfide bonds, cross-links.
uniprot_get_alphafold_confidence: - alphafold.ebi.ac.uk
uniprot_resolve_clinvar: - eutils.ncbi.nlm.nih.gov
uniprot_get_publications: - rest.uniprot.org
uniprot_resolve_orthology: - Group orthology cross-references by source DB (KEGG / OMA / OrthoDB / eggNOG / 8 more).
uniprot_get_evidence_summary: - Aggregate ECO codes (Evidence and Conclusion Ontology) across an entry and grade them into a 0-100 evidence-confidence score (high / moderate / low / very-low).
uniprot_target_dossier: - One-call comprehensive characterisation: nine sections - identity / function / chemistry / structure / drug-target / disease / variants / functional annotations
uniprot_provenance_verify: - Re-fetch a previously recorded URL and compare release tag + canonical response SHA-256. Five verdicts (verified, release_drift, hash_drift, release_and_hash_dr

Latest releases

v1.3.5 · 2026-08-21

1.3.5 (2026-08-20) · attest reproducible CycloneDX without detector mismatch

v1.3.4 · 2026-08-20

1.3.4 (2026-08-20) · lock provenance redirects to UniProt origin

v1.3.3 · 2026-08-10

1.3.3 (2026-08-10) · bind SBOM and registry publisher to immutable artifacts

04 · Who maintains Uniprot MCP

uniprot-mcp is maintained by smaniches. We track 3 MCP servers from smaniches - 3 actively maintained, 21 combined GitHub stars, oldest repo from Nov 2025. Full record: all servers from smaniches.

05 · Facts

repository: github.com/smaniches/uniprot-mcp
category: database - ranked #53 of 151 actively-maintained database servers as of 2026-08-25.
release cadence: 10+ releases in the last 90 days (latest 2026-08-21)
registry: io.github.smaniches/uniprot-mcp (active, first published 2026-06-09 · 11 versions)
packages: pypi:uniprot-mcp-server

06 · Uniprot MCP FAQ

Is Uniprot MCP still maintained?

Yes - as of 2026-08-25, its last commit was 2026-08-24 and it shipped 10+ releases in the last 90 days. We re-verify nightly.

What can Uniprot MCP do?

With this server connected, an agent can filter by organism / type / completeness, and index search across UniProt citations.

How do I install Uniprot MCP?

Run `uvx uniprot-mcp-server`. The README documents 2 environment variables (UNIPROT_MCP_CACHE_DIR, UNIPROT_PIN_RELEASE) to set first. Set UNIPROT_MCP_CACHE_DIR, UNIPROT_PIN_RELEASE before connecting. You can also paste the ready-made client config above.

Does Uniprot MCP run locally?

Yes - it's a stdio server: it runs on your machine (via uvx) with your user's permissions. Your data stays local unless the server itself calls external APIs.

07 · Alternatives to Uniprot MCP

Alternatives to Uniprot MCP

Maintained database servers if Uniprot MCP isn't the fit.

Pairs well with

Servers that cover what Uniprot MCP doesn't - only shown when the pairing reason fits the companion.

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