Tools reference

uniprot-mcp ships 41 tools across eight families. All read-only (readOnlyHint: true). All but uniprot_replay_from_cache interact with at least one upstream service (openWorldHint: true).

Core UniProtKB (10)

Tool	Purpose
uniprot_get_entry	Fetch full entry by accession.
uniprot_search	UniProt query language; filter by gene / organism / reviewed.
uniprot_get_sequence	FASTA with PIR-style provenance comment block.
uniprot_get_features	Domains / sites / PTMs / signal peptides.
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 (PDB / Pfam / Ensembl / Reactome / KEGG / STRING / …).
uniprot_id_mapping	Map IDs between databases.
uniprot_batch_entries	Up to 100 entries in one call; invalid accessions filtered client-side.
uniprot_taxonomy_search	Search UniProt taxonomy by organism name.

Controlled vocabularies (4)

Tool	Purpose
uniprot_get_keyword	Keyword by ID (e.g. KW-0007 = Acetylation).
uniprot_search_keywords	Free-text keyword search.
uniprot_get_subcellular_location	Subcellular-location term by ID (e.g. SL-0039 = Cell membrane).
uniprot_search_subcellular_locations	Free-text location search.

Sequence archives & clusters (4)

Tool	Purpose
uniprot_get_uniref	UniRef cluster by ID (UniRef50_P04637, etc.).
uniprot_search_uniref	Cluster search with identity_tier filter.
uniprot_get_uniparc	Sequence-archive record by UPI (UPI000002ED67).
uniprot_search_uniparc	UniParc full-text search.

Proteomes & literature (4)

Tool	Purpose
uniprot_get_proteome	Proteome by UP ID (UP000005640 = human). Counts, BUSCO, components.
uniprot_search_proteomes	Filter by organism / type / completeness.
uniprot_get_citation	Citation record by ID (typically PubMed).
uniprot_search_citations	Citation index search.

Structured cross-DB resolvers (4)

These extract cross-references from a UniProt entry and return structured records — typed lists / objects, not passthrough strings. Gateway-only — no calls leave the UniProt origin.

Tool	Purpose
uniprot_resolve_pdb	PDB structures: id + method + resolution + chain coverage.
uniprot_resolve_alphafold	AlphaFold model id + EBI viewer URL (model id only — for confidence call the dedicated tool below).
uniprot_resolve_interpro	InterPro signatures: id + entry name.
uniprot_resolve_chembl	ChEMBL drug-target id + EBI target-card URL.

Biomedical features (7)

Pure-Python compositions over the entry — no extra origin. The first four answer per-residue and per-variant questions; the last three are the v1.1.0 expansion targeting drug discovery, therapeutic-protein engineering, and pathogen-secretion analysis. Each is a structured filter over the entry's features array — it groups by feature type, shows the residue range and description for each member, and emits an honest empty-set advisory pointing at adjacent databases when the entry has no annotations of that kind.

Tool	Purpose
uniprot_compute_properties	Derived sequence chemistry: MW / pI / GRAVY / aromaticity / charge / ε₂₈₀. Pure-Python on the FASTA — no external API.
uniprot_features_at_position	Every feature overlapping a residue position (1-indexed). 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 + MIM 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 — input to enzyme drug-design and antibiotic-target-validation workflows.
uniprot_get_processing_features	Maturation features: signal peptide, propeptide, transit peptide, initiator methionine, chain, peptide. Therapeutic-protein engineering and pathogen-secretion-system analysis.
uniprot_get_ptms	Post-translational modifications: modified residues, glycosylation, lipidation, disulfide bonds, cross-links.

Cross-origin enrichment (3)

These are the only tools that consult origins outside rest.uniprot.org. Each is documented in PRIVACY.md and in the threat model.

Tool	Origin	Purpose
uniprot_get_alphafold_confidence	alphafold.ebi.ac.uk	Model-level mean pLDDT + four-band distribution. Exact accession matching, fragment ranges, and additional model summaries; not a per-residue confidence score.
uniprot_resolve_clinvar	eutils.ncbi.nlm.nih.gov	Human UniProt entries only (NCBI taxon 9606); ClinVar classifications by gene + optional protein change, not transferable to nonhuman orthologs.
uniprot_get_publications	rest.uniprot.org	Pure-Python over the entry's references — listed here because it complements the cross-origin enrichment.

Composition + provenance (5)

Tool	Purpose
uniprot_resolve_orthology	Group orthology cross-references by source DB (KEGG / OMA / OrthoDB / eggNOG / 8 more).
uniprot_get_evidence_summary	Summarize UniProt ECO annotation evidence and assertion methods, with a weighted 0-100 descriptive mix index. The index is uncalibrated, not a probability of annotation correctness and not comparable to AlphaFold pLDDT.
uniprot_target_dossier	One-call comprehensive characterisation: nine sections in one structured report.
uniprot_provenance_verify	Re-fetch a previously recorded URL and compare release + canonical SHA-256. Six verdicts (verified / incomplete_evidence / release_drift / hash_drift / release_and_hash_drift / url_unreachable).
uniprot_replay_from_cache	Read a cached UniProt response without hitting the upstream. Opt-in via UNIPROT_MCP_CACHE_DIR.

Cross-cutting input validation

Every tool that takes an identifier validates it before any HTTP call. The regexes are defined once in src/uniprot_mcp/client.py and shared:

Identifier	Regex
UniProt accession	\A(?:[OPQ][0-9][A-Z0-9]{3}[0-9]\|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2})\Z
Keyword	\AKW-[0-9]{4}\Z
Subcellular location	\ASL-[0-9]{4}\Z
UniRef cluster	\AUniRef(?:50\|90\|100)_(<acc>\|UPI<10 hex>)\Z
UniParc UPI	\AUPI[A-F0-9]{10}\Z
Proteome UP	\AUP[0-9]{9,11}\Z
Citation	\A[0-9]{1,12}\Z
HGVS shorthand	\A[ACDEFGHIKLMNPQRSTVWY][1-9][0-9]{0,4}[ACDEFGHIKLMNPQRSTVWY*]\Z (20 standard residues; * = stop; defined in server.py)

Length caps are also applied; see src/uniprot_mcp/server.py for the exact constants.

Output formats

Every tool accepts response_format="markdown" (default) or response_format="json".

• Markdown carries a trailing provenance footer (--- separator
• _Source:_ + _Query:_ + _SHA-256:_).
• JSON wraps the data in a {"data": ..., "provenance": ...} envelope.
• FASTA (sequence tool only) prepends a PIR-style ;-prefix comment block before the first > record — parser-safe for BLAST+, biopython, emboss.