Schema | uniprot-unipressed-mcp

uniprot-unipressed-mcp

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Server Configuration

Describes the environment variables required to run the server.

Name	Required	Description	Default
No arguments

Capabilities

Features and capabilities supported by this server

Capability	Details
`tools`	{ "listChanged": true }
`prompts`	{ "listChanged": false }
`resources`	{ "subscribe": false, "listChanged": false }
`experimental`	{ "tasks": { "list": {}, "cancel": {}, "requests": { "tools": { "call": {} }, "prompts": { "get": {} }, "resources": { "read": {} } } } }

Tools

Functions exposed to the LLM to take actions

Name Description

Name	Description
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.
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`

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.

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

Prompts

Interactive templates invoked by user choice

Name	Description
No prompts

Resources

Contextual data attached and managed by the client

Name	Description
No resources

Server Configuration
Capabilities
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Prompts
Resources

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