How do I connect Uniprot MCP Server to Claude?

Run `claude mcp add uniprot-mcp -- uvx uniprot-mcp-server` in Claude Code, or add the same command and arguments under mcpServers in Cursor's mcp.json or Claude Desktop's claude_desktop_config.json, then restart the client. The blocks above are ready to paste.

Is Uniprot MCP Server free?

The listed licence is Apache-2.0. Check the upstream terms for permitted use and commercial requirements; a public repository does not by itself mean the software is free or open source. Connected APIs and hosted services may have separate charges.

What can Uniprot MCP Server do?

Uniprot MCP Server documents 40 tools to the agent, including uniprot_batch_entries, uniprot_compute_properties, uniprot_features_at_position. The descriptions above come from project documentation. A live handshake does not test individual tool behavior.

Uniprot MCP

Unclaimed

by smaniches

Auditable UniProt MCP server with per-response SHA-256 provenance, release pinning, verification, and offline replay.

Set up this server

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01 / Choose your client

02 / Before you connect

Authentication is not specified. Check the project instructions before connecting.

Install the runtime required by the project and make it available to your client.

Project instructionsEnvironment variable names (optional)

Use names from the project instructions, separated by commas. Enter names only, never secret values.

03 / Add the configuration

Source: generated from public install instructions

claude mcp add --transport stdio 'uniprot-mcp' -- 'uvx' 'uniprot-mcp-server'

Run in your terminal after replacing any placeholders.

04 / Check it in your client

Open your client’s MCP settings and confirm the server connects and lists its tools. A copied configuration does not confirm a working connection.

bioinformaticsclaudeclaude-aiclaude-codeclinvar-databaseclinvar-database-mcpdrugdrug-designdrug-discoverydrug-repurposing

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Security profile

Claimed and verified servers get a weekly static scan that shows what the code can reach: external services, environment variables, shell commands, agent configuration folders, plus any dependencies with known advisories. Claim this listing to get one. How the security profile works

40 of 40 tools

Documented tools (40)

From project documentation. A server handshake does not verify each tool’s description or behavior.

uniprot_batch_entries

Up to 100 entries in one call; invalid accessions filtered client-side.

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_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_alphafold_confidence

alphafold.ebi.ac.uk

uniprot_get_citation

Citation record by ID (typically a PubMed numeric ID).

uniprot_get_cross_refs

Raw cross-references to PDB, Pfam, Ensembl, Reactome, KEGG, STRING …

uniprot_get_disease_associations

Structured disease records from DISEASE-type comments: name + acronym + UniProt disease ID + OMIM cross-ref + description.

uniprot_get_entry

Full UniProt entry (e.g. P04637 for p53). Function, gene, organism, disease, cross-refs.

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). Distinguishes wet-lab confirmed from inferred-by-similarity from automatic.

uniprot_get_features

Domains, binding sites, PTMs, signal peptides — optional type filter.

uniprot_get_go_terms

GO annotations grouped by aspect (F / P / C).

uniprot_get_keyword

Keyword by ID (e.g. KW-0007 = Acetylation). Definition, synonyms, GO refs, hierarchy.

uniprot_get_processing_features

Maturation features: signal peptide, propeptide, transit peptide, initiator methionine, chain, peptide. Essential for therapeutic-protein engineering and pathogen-secretion analysis.

uniprot_get_proteome

Proteome by UP ID (UP000005640 = human). Counts, BUSCO score, components.

uniprot_get_ptms

Post-translational modifications: modified residues (phospho/acetyl/methyl), glycosylation, lipidation (GPI/prenyl/palmitoyl), disulfide bonds, cross-links.

uniprot_get_publications

rest.uniprot.org

uniprot_get_sequence

FASTA. PIR-style provenance comment block above the first record (BLAST+ / biopython compatible).

uniprot_get_subcellular_location

Subcellular-location term by ID (e.g. SL-0039 = Cell membrane).

uniprot_get_uniparc

Sequence-archive record by UPI (UPI000002ED67).

uniprot_get_uniref

UniRef cluster by ID (UniRef50P04637, UniRef90P04637, UniRef100P04637).

uniprot_get_variants

Natural variants and disease mutations.

uniprot_id_mapping

Map IDs between databases (GeneName → UniProtKB, PDB → UniProtKB, …).

uniprot_lookup_variant

HGVS-shorthand match (R175H, V600E, R248) against UniProt's natural-variant features.

uniprot_provenance_verify

Re-fetch a previously recorded URL and compare release tag + canonical response SHA-256. Five verdicts (verified, releasedrift, hashdrift, releaseandhashdrift, urlunreachable) each with an advice string.

uniprot_resolve_alphafold

AlphaFold model id + EBI viewer URL (model id only — for pLDDT call the dedicated tool below).

uniprot_resolve_chembl

ChEMBL drug-target id + EBI target-card URL.

uniprot_resolve_clinvar

eutils.ncbi.nlm.nih.gov

uniprot_resolve_interpro

InterPro signatures: id + entry name.

uniprot_resolve_orthology

Group orthology cross-references by source DB (KEGG / OMA / OrthoDB / eggNOG / 8 more).

uniprot_resolve_pdb

PDB structures: id + method + resolution + chain coverage.

uniprot_search

UniProt query language — gene, organism, taxon ID, reviewed flag, free text.

uniprot_search_citations

Index search across UniProt citations.

uniprot_search_keywords

Free-text keyword search.

uniprot_search_proteomes

Filter by organism / type / completeness.

uniprot_search_subcellular_locations

Free-text location search.

uniprot_search_uniparc

UniParc full-text search.

uniprot_search_uniref

Cluster search with identitytier filter (50 / 90 / 100).

uniprot_target_dossier

One-call comprehensive characterisation: nine sections — identity / function / chemistry / structure / drug-target / disease / variants / functional annotations / cross-refs.

uniprot_taxonomy_search

Search UniProt taxonomy by organism name.

Tool change history

Compared across complete checks of the same configuration. Tools were listed, not invoked. Input-schema changes are not measured here.

No complete tool checks yet.

FAQ

Questions about Uniprot MCP Server

How do I connect Uniprot MCP Server to Claude?: Run `claude mcp add uniprot-mcp -- uvx uniprot-mcp-server` in Claude Code, or add the same command and arguments under mcpServers in Cursor's mcp.json or Claude Desktop's claude_desktop_config.json, then restart the client. The blocks above are ready to paste.
Is Uniprot MCP Server free?: The listed licence is Apache-2.0. Check the upstream terms for permitted use and commercial requirements; a public repository does not by itself mean the software is free or open source. Connected APIs and hosted services may have separate charges.
What can Uniprot MCP Server do?: Uniprot MCP Server documents 40 tools to the agent, including uniprot_batch_entries, uniprot_compute_properties, uniprot_features_at_position. The descriptions above come from project documentation. A live handshake does not test individual tool behavior.