How do I use uniprot-unipressed-mcp?

1. Click on "Install Server". 2. Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state. 3. In the chat, type @ followed by the MCP server name and your instructions, e.g., "@uniprot-unipressed-mcp search for human BRCA1 protein" That's it! The server will respond to your query, and you can continue using it as needed. Here is a step-by-step guide with screenshots.

uniprot-unipressed-mcp

by pansapiens

Overview Schema Related Servers Score Discussions

Python

Remote

UniProt MCP Server

An MCP (Model Context Protocol) server that provides tools for querying the UniProt protein database using the unipressed Python library.

Features

Search proteins using standard the UniProt query syntax across UniProtKB, UniParc, or UniRef databases
Fetch specific entries by accession ID
Pagination for large result sets
Field selection to control returned data
JSON format responses by default - responses are returned in JSON format, with TOON format available as an option

Related MCP server: UniProt MCP Server

Installation

Using uv (recommended)

uv sync

This will create a virtual environment and install all dependencies.

Development installation

uv sync --extra dev

This installs the package with development dependencies (pytest, etc.).

Usage

Running the server

With uvx (recommended)

uvx uniprot-unipressed-mcp

Or from a git repository:

uvx --from git+https://github.com/pansapiens/uniprot-unipressed-mcp uniprot-mcp

Alternative example: with the FastMCP CLI and HTTP transport

fastmcp run src/uniprot_mcp/server.py:mcp --transport http --port 8007

Configuring with MCP clients

Claude Code

Add the server using the Claude Code CLI:

claude mcp add uniprot-unipressed-mcp -- uvx git+https://github.com/pansapiens/uniprot-unipressed-mcp

Other MCP clients

Or manually add to your MCP configuration (Claude Code, Cursor, etc.):

{
  "mcpServers": {
    "uniprot-unipressed-mcp": {
      "command": "uvx",
      "args": ["git+https://github.com/pansapiens/uniprot-unipressed-mcp"]
    }
  }
}

Response Format

Tool responses are returned in JSON format by default. To receive TOON format responses instead, use the response_format parameter with value "toon":

# JSON format (default)
result = uniprot_search(query="gene:BRCA1")

# TOON format
result = uniprot_search(query="gene:BRCA1", response_format="toon")

Tools

uniprot_search

Search the UniProt protein database using query syntax.

Parameters:

Parameter	Type	Required	Default	Description
query	string	Yes	-	UniProt query string
database	string	No	"uniprotkb"	Database to search: uniprotkb, uniparc, uniref
limit	integer	No	10	Results per page (1-100)
fields	list[string]	No	None	Return fields to include
cursor	string	No	None	Pagination cursor from previous result
response_format	string	No	"json"	Response format: "json" (default) or "toon"

Example queries:

gene:BRCA1                              # Search by gene name
organism_id:9606                        # Human proteins (NCBI taxonomy ID)
(gene:BRCA*) AND (organism_id:10090)    # Mouse BRCA genes with wildcard
length:[500 TO 700]                     # Proteins of specific length range
keyword:kinase                          # By UniProt keyword
family:serpin                           # By protein family
ec:3.2.1.23                             # By enzyme classification
reviewed:true                           # Only Swiss-Prot reviewed entries

Response:

By default, responses are returned in JSON format. When response_format="toon" is specified, responses are returned in TOON format (a compact string):

JSON format (default):

{
  "results": [...],
  "total": 1234,
  "nextCursor": "eyJvZmZzZXQiOiAxMH0="
}

TOON format:

results[10]:
  - entryType: UniProtKB reviewed (Swiss-Prot)
    primaryAccession: P38398
    secondaryAccessions[7]: E9PFZ0,O15129,Q1RMC1,Q3LRJ0,Q3LRJ6,Q6IN79,Q7KYU9
    uniProtkbId: BRCA1_HUMAN
    ...etc...

uniprot_fetch

Fetch specific protein entries by their UniProt accession IDs.

Parameters:

Parameter	Type	Required	Default	Description
ids	list[string]	Yes	-	UniProt accession IDs to fetch
database	string	No	"uniprotkb"	Database to fetch from
fields	list[string]	No	None	Return fields to include
response_format	string	No	"json"	Response format: "json" (default) or "toon"

Example:

uniprot_fetch(ids=["P62988", "A0A0C5B5G6"])

Response:

By default, responses are returned in JSON format. When response_format="toon" is specified, responses are returned in TOON format (a compact string):

JSON format (default):

{
  "results": [...],
  "found": 2,
  "requested": 2
}

TOON format:

results[10]:
  - entryType: UniProtKB reviewed (Swiss-Prot)
    primaryAccession: P38398
    secondaryAccessions[7]: E9PFZ0,O15129,Q1RMC1,Q3LRJ0,Q3LRJ6,Q6IN79,Q7KYU9
    uniProtkbId: BRCA1_HUMAN
    ...etc...

Pagination

The server uses cursor-based pagination for search results. When more results are available, the response includes a nextCursor field. Pass this cursor in subsequent requests to retrieve the next page:

# First request
result1 = uniprot_search(query="organism_id:9606", limit=10)

# Get next page using cursor
if "nextCursor" in result1:
    result2 = uniprot_search(
        query="organism_id:9606",
        limit=10,
        cursor=result1["nextCursor"]
    )

Databases

Database	Description
uniprotkb	UniProt Knowledgebase - curated protein sequences and annotations
uniparc	UniProt Archive - comprehensive protein sequence archive
uniref	UniProt Reference Clusters - clustered protein sequences

Return Fields

Common return fields include:

accession - UniProt accession number
id - Entry name
gene_names - Gene names
protein_name - Protein names
organism_name - Source organism
organism_id - NCBI taxonomy ID
length - Sequence length
mass - Molecular mass
sequence - Amino acid sequence
cc_function - Function annotation
cc_subcellular_location - Subcellular location

See the UniProt return fields documentation for the complete list.

Development

Using a local copy of the repository

{
  "mcpServers": {
    "uniprot-unipressed-mcp": {
      "command": "uv",
      "args": ["--directory", "/path/to/uniprot-unipressed-mcp", "run", "-m", "uniprot_mcp.server"]
    }
  }
}

Testing using the MCP Inspector

npx @modelcontextprotocol/inspector uv --directory $(pwd) run -m uniprot_mcp.server

Running tests

uv run pytest

This runs all unit tests. Integration tests (which require network access to the UniProt API) are skipped by default.

Running integration tests

Integration tests can be enabled using an environment variable:

RUN_INTEGRATION_TESTS=1 uv run pytest

Or run only integration tests:

RUN_INTEGRATION_TESTS=1 uv run pytest -m integration

Running tests with coverage

uv run pytest --cov=uniprot_mcp

To include integration tests in coverage:

RUN_INTEGRATION_TESTS=1 uv run pytest --cov=uniprot_mcp

Resources

UniProt
UniProt Query Syntax
UniProt Return Fields
unipressed Documentation
FastMCP Documentation
Model Context Protocol
TOON Format - Alternative serialization format available as an option

Licence

MIT

Available Tools

2 tools

uniprot_fetchA

Fetch specific protein entries by their UniProt accession IDs.

Args: ids: List of UniProt accession IDs to fetch. Examples: - ["P62988"] - Single protein - ["A0A0C5B5G6", "A0A1B0GTW7"] - Multiple proteins

database: UniProt database to fetch from. One of: uniprotkb (default), uniparc, uniref

fields: Optional list of return fields to include. If not specified, all fields
    are returned. Available return fields (see https://www.uniprot.org/help/return_fields):
    
    Names & Taxonomy:
    - accession, id, gene_names, gene_primary, gene_synonym, gene_oln, gene_orf
    - organism_name, organism_id, protein_name, xref_proteomes
    - lineage, lineage_ids, virus_hosts
    
    Sequences:
    - cc_alternative_products, ft_var_seq, cc_sc_epred, fragment, encoded_in
    - length, mass, cc_mass_spectrometry, ft_variant, ft_non_cons, ft_non_std
    - ft_non_ter, cc_polymorphism, cc_rna_editing, sequence, cc_sequence_caution
    - ft_conflict, ft_unsure, sequence_version
    
    Function:
    - absorption, ft_act_site, cc_activity_regulation, ft_binding, cc_catalytic_activity
    - cc_cofactor, ft_dna_bind, ec, cc_function, kinetics, cc_pathway
    - ph_dependence, redox_potential, rhea, ft_site, temp_dependence
    
    Miscellaneous:
    - annotation_score, cc_caution, comment_count, feature_count, keywordid, keyword
    - cc_miscellaneous, protein_existence, reviewed, tools, uniparc_id
    
    Interaction:
    - cc_interaction, cc_subunit
    
    Expression:
    - cc_developmental_stage, cc_induction, cc_tissue_specificity
    
    Gene Ontology (GO):
    - go_p, go_c, go, go_f, go_id
    
    Pathology & Biotech:
    - cc_allergen, cc_biotechnology, cc_disruption_phenotype, cc_disease
    - ft_mutagen, cc_pharmaceutical, cc_toxic_dose
    
    Subcellular location:
    - ft_intramem, cc_subcellular_location, ft_topo_dom, ft_transmem
    
    PTM / Processing:
    - ft_chain, ft_crosslnk, ft_disulfid, ft_carbohyd, ft_init_met, ft_lipid
    - ft_mod_res, ft_peptide, cc_ptm, ft_propep, ft_signal, ft_transit
    
    Structure:
    - structure_3d, ft_strand, ft_helix, ft_turn
    
    Publications:
    - lit_pubmed_id
    
    Date:
    - date_created, date_modified, date_sequence_modified, version
    
    Family & Domains:
    - ft_coiled, ft_compbias, cc_domain, ft_domain, ft_motif, protein_families
    - ft_region, ft_repeat, ft_zn_fing
    
    Cross-references:
    - See https://www.uniprot.org/help/return_fields for cross-reference fields

response_format: Response format. One of: 'json' (default) or 'toon'.
    - 'json': Returns response in JSON format
    - 'toon': Returns response in TOON format

Returns: When response_format='json': JSON object with: - results: Array of fetched protein entries - found: Number of entries successfully retrieved - requested: Number of IDs that were requested

When response_format='toon': TOON-formatted string with:
- results: Array of fetched protein entries
- found: Number of entries successfully retrieved
- requested: Number of IDs that were requested

ParametersJSON Schema

Name	Required	Default
`ids`	Yes
`database`	No	uniprotkb
`fields`	No
`response_format`	No	json

Output Schema

ParametersJSON Schema

Name	Required	Description
`result`	Yes

TDQS

A3.6/5.0

Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, and the description lacks disclosure of behavioral traits such as rate limits, authentication requirements, or error handling for missing IDs. It only describes the return format but not edge cases or limitations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness3/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is well-structured with clear sections (Args, Returns), but it is overly verbose due to the exhaustive list of fields. This could be shortened or referenced externally for better conciseness.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the absence of annotations and an output schema, the description provides adequate information about parameters and return format. However, it lacks details on error handling, performance considerations, or rate limits, leaving some gaps for a complete understanding.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 0%, so the description fully compensates by providing detailed parameter explanations, including examples, defaults, allowed values (enum for database and response_format), and an extensive list of available fields with categories.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states 'Fetch specific protein entries by their UniProt accession IDs,' which is a specific verb+resource combination. It clearly differentiates from the sibling tool 'uniprot_search' by focusing on fetching by ID rather than searching.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description does not explicitly specify when to use this tool versus alternatives. While the sibling name implies search vs. fetch, there is no guidance on when to choose one over the other or any conditions or prerequisites.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

uniprot_searchA

Search the UniProt protein database using query syntax.

Args: query: UniProt query string. Examples: - gene:BRCA1 - Search by gene name - organism_id:9606 - Human proteins (NCBI taxonomy ID) - (gene:BRCA*) AND (organism_id:10090) - Mouse BRCA genes with wildcard - length:[500 TO 700] - Proteins of specific length range - keyword:kinase - By UniProt keyword - family:serpin - By protein family - ec:3.2.1.23 - By enzyme classification - database:pfam - With Pfam cross-references - reviewed:true - Only Swiss-Prot reviewed entries

    Available query fields (see https://www.uniprot.org/help/query-fields):
    - accession: Primary/canonical isoform accessions (e.g., accession:P62988)
    - active: Active/obsolete status (e.g., active:false)
    - lit_author: Reference author (e.g., lit_author:ashburner)
    - protein_name: Protein name (e.g., protein_name:CD233)
    - chebi: ChEBI identifier (e.g., chebi:18420)
    - xrefcount_pdb: Cross-reference count (e.g., xref_count_pdb:[20 TO *])
    - date_created: Creation date (e.g., date_created:[2012-10-01 TO *])
    - date_modified: Last modification date (e.g., date_modified:[2012-01-01 TO 2019-03-01])
    - date_sequence_modified: Sequence modification date (e.g., date_sequence_modified:[2012-01-01 TO 2012-03-01])
    - database: Database cross-reference (e.g., database:pfam)
    - xref: Cross-reference (e.g., xref:pdb-1aut)
    - ec: Enzyme Commission number (e.g., ec:3.2.1.23)
    - existence: Protein existence level (e.g., existence:3)
    - family: Protein family (e.g., family:serpin)
    - fragment: Fragment status (e.g., fragment:true)
    - gene: Gene name (e.g., gene:HPSE)
    - gene_exact: Exact gene name (e.g., gene_exact:HPSE)
    - go: Gene Ontology term (e.g., go:0015629)
    - virus_host_name: Virus host name
    - virus_host_id: Virus host ID (e.g., virus_host_id:10090)
    - accession_id: Primary accession (e.g., accession_id:P00750)
    - inchikey: InChIKey identifier (e.g., inchikey:WQZGKKKJIJFFOK-GASJEMHNSA-N)
    - interactor: Interacting protein (e.g., interactor:P00520)
    - keyword: Keyword (e.g., keyword:toxin or keyword:KW-0800)
    - length: Sequence length range (e.g., length:[500 TO 700])
    - mass: Molecular mass range (e.g., mass:[500000 TO *])
    - cc_mass_spectrometry: Mass spectrometry method (e.g., cc_mass_spectrometry:maldi)
    - encoded_in: Gene location (e.g., encoded_in:Mitochondrion)
    - organism_name: Organism name (e.g., organism_name:"Ovis aries")
    - organism_id: Organism taxonomy ID (e.g., organism_id:9940)
    - plasmid: Plasmid name (e.g., plasmid:ColE1)
    - proteome: Proteome ID (e.g., proteome:UP000005640)
    - proteomecomponent: Proteome component (e.g., proteomecomponent:"chromosome 1")
    - sec_acc: Secondary accession (e.g., sec_acc:P02023)
    - reviewed: Reviewed status (e.g., reviewed:true)
    - scope: Reference scope (e.g., scope:mutagenesis)
    - sequence: Sequence identifier (e.g., accession:P05067-9 AND is_isoform:true)
    - strain: Organism strain (e.g., strain:wistar)
    - taxonomy_name: Taxonomy name (e.g., taxonomy_name:mammal)
    - taxonomy_id: Taxonomy ID (e.g., taxonomy_id:40674)
    - tissue: Tissue type (e.g., tissue:liver)
    - cc_webresource: Web resource (e.g., cc_webresource:wikipedia)
    
database: UniProt database to search. One of: uniprotkb (default), uniparc, uniref

limit: Maximum number of results per page (1-100, default 10)

fields: Optional list of return fields to include. If not specified, all fields
    are returned. Available return fields (see https://www.uniprot.org/help/return_fields):
    
    Names & Taxonomy:
    - accession, id, gene_names, gene_primary, gene_synonym, gene_oln, gene_orf
    - organism_name, organism_id, protein_name, xref_proteomes
    - lineage, lineage_ids, virus_hosts
    
    Sequences:
    - cc_alternative_products, ft_var_seq, cc_sc_epred, fragment, encoded_in
    - length, mass, cc_mass_spectrometry, ft_variant, ft_non_cons, ft_non_std
    - ft_non_ter, cc_polymorphism, cc_rna_editing, sequence, cc_sequence_caution
    - ft_conflict, ft_unsure, sequence_version
    
    Function:
    - absorption, ft_act_site, cc_activity_regulation, ft_binding, cc_catalytic_activity
    - cc_cofactor, ft_dna_bind, ec, cc_function, kinetics, cc_pathway
    - ph_dependence, redox_potential, rhea, ft_site, temp_dependence
    
    Miscellaneous:
    - annotation_score, cc_caution, comment_count, feature_count, keywordid, keyword
    - cc_miscellaneous, protein_existence, reviewed, tools, uniparc_id
    
    Interaction:
    - cc_interaction, cc_subunit
    
    Expression:
    - cc_developmental_stage, cc_induction, cc_tissue_specificity
    
    Gene Ontology (GO):
    - go_p, go_c, go, go_f, go_id
    
    Pathology & Biotech:
    - cc_allergen, cc_biotechnology, cc_disruption_phenotype, cc_disease
    - ft_mutagen, cc_pharmaceutical, cc_toxic_dose
    
    Subcellular location:
    - ft_intramem, cc_subcellular_location, ft_topo_dom, ft_transmem
    
    PTM / Processing:
    - ft_chain, ft_crosslnk, ft_disulfid, ft_carbohyd, ft_init_met, ft_lipid
    - ft_mod_res, ft_peptide, cc_ptm, ft_propep, ft_signal, ft_transit
    
    Structure:
    - structure_3d, ft_strand, ft_helix, ft_turn
    
    Publications:
    - lit_pubmed_id
    
    Date:
    - date_created, date_modified, date_sequence_modified, version
    
    Family & Domains:
    - ft_coiled, ft_compbias, cc_domain, ft_domain, ft_motif, protein_families
    - ft_region, ft_repeat, ft_zn_fing
    
    Cross-references:
    - See https://www.uniprot.org/help/return_fields for cross-reference fields
    
cursor: Pagination cursor from a previous search result's 'nextCursor' field.
    Pass this to retrieve the next page of results.

response_format: Response format. One of: 'json' (default) or 'toon'.
    - 'json': Returns response in JSON format
    - 'toon': Returns response in TOON format

Returns: When response_format='json': JSON object with: - results: Array of matching protein entries - total: Total number of matching entries (if available) - nextCursor: Cursor string for retrieving the next page (if more results exist)

When response_format='toon': TOON-formatted string with:
- results: Array of matching protein entries
- total: Total number of matching entries (if available)
- nextCursor: Cursor string for retrieving the next page (if more results exist)

See https://www.uniprot.org/help/query-fields for full query syntax documentation.

ParametersJSON Schema

Name	Required	Default
`query`	Yes
`database`	No	uniprotkb
`limit`	No
`fields`	No
`cursor`	No
`response_format`	No	json

Output Schema

ParametersJSON Schema

Name	Required	Description
`result`	Yes

TDQS

A4.3/5.0

Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description carries full burden. It explains that the tool queries UniProt databases, supports pagination via cursor, and describes response formats. It does not mention destructive behavior or rate limits, but for a search tool this is acceptable and transparent.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is lengthy but well-structured with sections for query syntax, parameters, and return values. It is front-loaded with the basic purpose. While not concise, the structure makes it easy to navigate, and all information is relevant given the tool's complexity.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool's complexity (multiple databases, extensive query fields, pagination, response format), the description is complete. It covers all parameters, explains output schema with results, total, and nextCursor, and provides links to external documentation.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The schema has 0% description coverage, but the description compensates fully by detailing each parameter: query with numerous examples, database with allowed values, limit with range, fields with a categorized list, cursor for pagination, and response_format with enum values and descriptions. This adds significant meaning beyond the schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states it searches the UniProt protein database using query syntax, with a specific verb and resource. The sibling tool name 'uniprot_fetch' implies a fetch operation, so the search purpose is distinct and clear.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

While the description provides extensive query examples and lists available fields, it does not explicitly state when to use this tool versus the sibling 'uniprot_fetch' tool. There is no guidance on when not to use it, leaving the agent to infer usage context from examples.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Install Server

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TDQS

A3.9/5.0

Disambiguation5/5

Each tool has a clearly distinct purpose: uniprot_fetch retrieves specific entries by IDs, while uniprot_search performs complex queries. There is no overlap in functionality.

Naming Consistency5/5

Both tool names follow a consistent verb_noun pattern with snake_case (uniprot_fetch, uniprot_search), making them predictable and easy to understand.

Tool Count3/5

With only 2 tools, the server is very thin for the vast UniProt domain. While fetch and search are core operations, the lack of other tools (e.g., for updates or batch operations) makes it feel limited.

Completeness3/5

The server covers basic retrieval operations (fetch by ID and search) but lacks any write or update functionality. For a read-only interface this might be acceptable, but tools for batch processing or data submission are missing.

Maintenance

ActivityInactive

ResponsivenessSyncing

Resources

GitHub Repository

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UniProt MCP Server

Features

Installation

Using uv (recommended)

Development installation

Usage

Running the server

With uvx (recommended)

Alternative example: with the FastMCP CLI and HTTP transport

Configuring with MCP clients

Claude Code

Other MCP clients

Response Format

Tools

uniprot_search

uniprot_fetch

Pagination

Databases

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