Pathway, interaction, protein and structure queries: parameters and notes

See the tutorial for usage and examples.

Each function includes its purpose, API, inputs, outputs, example code and result description. Prepare any required credentials, local files and optional dependencies; remote results vary with database releases and query time.

Retrieve stored AlphaFold protein structure predictions

dnakit.databases.alphafold_get_prediction(*, qualifier=None, uniprot_id=None, uniprot_accession=None, accession=None, sequence_checksum=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
qualifier	string	None	UniProt ACCESSION (e.g., 'P69905'). Do NOT use entry names like 'HBA_HUMAN'. Aliases: uniprot_id, uniprot_accession.
uniprot_id	string	None	Alias for qualifier: UniProt accession (e.g., 'P69905').
uniprot_accession	string	None	Alias for qualifier: UniProt accession (e.g., 'P69905').
accession	string	None	Alias for qualifier. UniProt accession (e.g., 'P04637') -- the same parameter name the UniProt_*_by_accession tools use.
sequence_checksum	string	None	Optional CRC64 checksum of the UniProt sequence.
verbose	bool	True	Progress flag.

Retrieve experimentally supported protein and genetic interactions

dnakit.databases.bio_grid_get_interactions(*, gene_names=None, gene_name=None, organism=None, interaction_type=None, evidence_types=None, limit=None, throughput=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_names	array	None	List of gene names or protein identifiers (e.g., ['TP53', 'BRCA1', 'MYC']). Accepts official gene symbols. {"items": {"type": "string"}, "minItems": 1}
gene_name	string	None	Alias for gene_names: single gene symbol (e.g., 'TP53'). Converted to gene_names list automatically.
organism	string	None	Organism name (e.g., 'Homo sapiens', 'Mus musculus') or NCBI taxonomy ID (e.g., '9606' for human, '10090' for mouse). Default: 9606 (human)
interaction_type	string	None	Type of interaction: 'physical' (protein-protein), 'genetic' (epistasis, synthetic lethality), 'both' (all interactions)
evidence_types	array	None	Filter by evidence types (e.g., ['Affinity Capture-MS', 'Two-hybrid'] for physical, ['Synthetic Lethality', 'Dosage Rescue'] for genetic). Leave empty for all evidence types. {"items": {"type": "string"}}
limit	integer	None	Maximum number of interactions to return (default: 100, max: 10000)
throughput	string	None	Filter by throughput: 'low' (low-throughput studies), 'high' (high-throughput screens), or leave empty for all
verbose	bool	True	Progress flag.

Configure before running: BIOGRID_ACCESS_KEY.

Search pathogen B-cell and T-cell epitopes

dnakit.databases.bvbrc_search_epitopes(*, taxon_id=None, protein_name=None, epitope_type=None, organism=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
taxon_id	string | null	None	NCBI Taxonomy ID for the pathogen organism. Examples: '2697049' (SARS-CoV-2), '11320' (Influenza A), '1773' (M. tuberculosis).
protein_name	string | null	None	Target protein name to filter epitopes. Examples: 'Spike glycoprotein', 'Nucleocapsid protein', 'Replicase polyprotein 1ab'.
epitope_type	string | null	None	Type of epitope. Options: 'Linear peptide', 'Discontinuous peptide'. Most epitopes are linear peptides.
organism	string | null	None	Organism name keyword to search across epitope records. Example: 'coronavirus', 'influenza'.
limit	integer | null	None	Maximum number of results. Default: 25. Max: 100.
verbose	bool	True	Progress flag.

Retrieve GO annotations for a gene or protein

dnakit.databases.go_get_annotations_for_gene(*, gene_id, rows=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_id	string	Required	A gene identifier such as gene symbol (e.g., 'TP53') or database ID.
rows	integer	None	Maximum number of annotation rows to return. Default: 100. Raise it (e.g. 2000) for a heavily annotated gene such as TP53, which has 1812 annotation rows; lower it to keep responses small.
verbose	bool	True	Progress flag.

Search GO terms by keyword

dnakit.databases.go_search_terms(*, query, verbose=True)

Parameter	Type	Required / default	Description and constraints
query	string	Required	The keyword to search for, e.g., 'apoptosis' or 'kinase activity'.
verbose	bool	True	Progress flag.

Retrieve tissue-specific protein interaction networks

dnakit.databases.humanbase_ppi_analysis(*, gene_list=None, tissue=None, max_node=None, interaction=None, string_mode=None, genes=None, top_n=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_list	array	None	List of gene names or symbols to analyze for protein-protein interactions. The gene name should be the official gene symbol, not the synonym. {"items": {"type": "string"}, "minItems": 1}
tissue	string	None	Tissue type for tissue-specific interactions. Use simple names like 'brain', 'heart', 'liver', 'kidney', 'lung', 'blood'. For v3 networks with more cell-type specificity, append '-v3' (e.g., 'brain-v3', 'liver-v3').
max_node	integer	None	Maximum number of nodes to retrieve in the interaction network. Warning: the more nodes, the more time it takes to retrieve the data. Default is 10 (~30 seconds).
interaction	string	None	Specific interaction type to filter by. Available types: 'co-expression', 'interaction', 'tf-binding', 'gsea-microrna-targets', 'gsea-perturbations'. If not specified, all types will be included.
string_mode	boolean	None	Whether to return the result in string mode. If True, the result will be a string of the network graph and the biological processes. If False, the result will be a NetworkX graph and a list of biological processes.
genes	array	None	Alias for gene_list. List of gene symbols to analyze. {"items": {"type": "string"}}
top_n	integer	None	Alias for max_node. Maximum number of network nodes to retrieve.
verbose	bool	True	Progress flag.

Retrieve antigens linked to an immune epitope

dnakit.databases.iedb_get_epitope_antigens(*, structure_id, limit=None, offset=None, order=None, select=None, filters=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
structure_id	integer	Required	IEDB epitope structure ID (from iedb_search_epitopes).
limit	integer	None	Maximum number of rows to return.
offset	integer	None	Pagination offset.
order	string	None	Optional PostgREST order clause.
select	object | None	None	Optional projection list (comma-separated string or array of field names). {"anyOf": [{"type": "string"}, {"type": "array", "items": {"type": "string"}}]}
filters	object	None	Advanced PostgREST filters mapping column -> filter expression. {"additionalProperties": {"type": "string"}}
verbose	bool	True	Progress flag.

Retrieve epitope MHC restriction associations

dnakit.databases.iedb_get_epitope_mhc(*, structure_id, limit=None, offset=None, order=None, select=None, filters=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
structure_id	integer	Required	IEDB epitope structure ID (from iedb_search_epitopes).
limit	integer	None	Maximum number of rows to return.
offset	integer	None	Pagination offset.
order	string	None	Optional PostgREST order clause.
select	object | None	None	Optional projection list (comma-separated string or array of field names). {"anyOf": [{"type": "string"}, {"type": "array", "items": {"type": "string"}}]}
filters	object	None	Advanced PostgREST filters mapping column -> filter expression. {"additionalProperties": {"type": "string"}}
verbose	bool	True	Progress flag.

Search B-cell epitope assay records

dnakit.databases.iedb_search_bcell(*, limit=None, offset=None, order=None, select=None, filters=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
limit	integer	None	Maximum number of rows to return.
offset	integer	None	Pagination offset.
order	string	None	Optional PostgREST order clause.
select	object | None	None	Optional projection list (comma-separated string or array of field names). {"anyOf": [{"type": "string"}, {"type": "array", "items": {"type": "string"}}]}
filters	object	None	Advanced PostgREST filters mapping column -> filter expression. {"additionalProperties": {"type": "string"}}
verbose	bool	True	Progress flag.

Search immune epitopes and their structure identifiers

dnakit.databases.iedb_search_epitopes(*, sequence_contains=None, structure_type=None, limit=None, offset=None, order=None, select=None, filters=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
sequence_contains	string	None	Sequence fragment to search within linear_sequence using a contains match. Example: 'KVF' finds epitopes containing that motif.
structure_type	string	None	Filter by epitope structure type. Example: 'Linear peptide'.
limit	integer	None	Maximum number of rows to return.
offset	integer	None	Pagination offset.
order	string	None	Optional PostgREST order clause (e.g., 'structure_id.asc').
select	object | None	None	Optional projection list to reduce payload size. Provide a comma-separated string or an array of field names (e.g., ['structure_id','linear_sequence']). {"anyOf": [{"type": "string"}, {"type": "array", "items": {"type": "string"}}]}
filters	object	None	Advanced PostgREST filters mapping column -> filter expression (e.g., {"linear_sequence":"ilike.KVF"}). {"additionalProperties": {"type": "string"}}
verbose	bool	True	Progress flag.

Search MHC-related assay records

dnakit.databases.iedb_search_mhc(*, limit=None, offset=None, order=None, select=None, filters=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
limit	integer	None	Maximum number of rows to return.
offset	integer	None	Pagination offset.
order	string	None	Optional PostgREST order clause.
select	object | None	None	Optional projection list (comma-separated string or array of field names). {"anyOf": [{"type": "string"}, {"type": "array", "items": {"type": "string"}}]}
filters	object	None	Advanced PostgREST filters mapping column -> filter expression. {"additionalProperties": {"type": "string"}}
verbose	bool	True	Progress flag.

Search T-cell response assays

dnakit.databases.iedb_search_tcell_assays(*, sequence=None, sequence_contains=None, mhc_class=None, qualitative_measure=None, limit=None, offset=None, select=None, filters=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
sequence	string	None	Exact peptide sequence to search (e.g., GILGFVFTL for influenza M1 epitope).
sequence_contains	string	None	Partial peptide sequence (substring match). Example: 'SIINFEKL'.
mhc_class	string	None	MHC class restriction (I or II).
qualitative_measure	string	None	Filter by assay result.
limit	integer	None	Maximum rows to return.
offset	integer	None	Pagination offset.
select	object | None	None	Columns to return (array of strings). Example: ['tcell_id','linear_sequence','mhc_restriction','qualitative_measure']. {"oneOf": [{"type": "string"}, {"type": "array", "items": {"type": "string"}}]}
filters	object	None	Advanced PostgREST filters (e.g., {"source_organism_iri":"eq.NCBITaxon:11320"}). {"additionalProperties": {"type": "string"}}
verbose	bool	True	Progress flag.

Retrieve immunogenetics resources and gene naming conventions

dnakit.databases.imgt_get_gene_info(*, operation=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Provider operation mode; see this row's default and allowed values.
verbose	bool	True	Progress flag.

Locate immunoglobulin and TCR germline gene searches

dnakit.databases.imgt_search_genes(*, operation=None, query=None, gene_type=None, species=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Provider operation mode; see this row's default and allowed values.
query	string	None	Search query (gene name)
gene_type	string	None	Gene type: IGHV, IGHD, IGHJ, IGKV, IGLV, TRAV, TRBV, etc.
species	string	None	Species name (default: Homo sapiens)
verbose	bool	True	Progress flag.

Search immunology studies by disease and assay

dnakit.databases.imm_port_search_studies(*, query, condition_or_disease=None, assay_method=None, research_focus=None, species=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
query	string	Required	Search keywords (e.g., 'influenza vaccine', 'COVID-19', 'T cell response', 'malaria')
condition_or_disease	string	None	Filter by disease/condition (e.g., 'influenza', 'malaria', 'HIV', 'dengue', 'tuberculosis'). Client-side substring match.
assay_method	string	None	Filter by assay method (e.g., 'Flow Cytometry', 'ELISPOT', 'RNA sequencing', 'ELISA', 'CyTOF', 'Luminex xMAP'). Client-side substring match.
research_focus	string	None	Filter by research focus (e.g., 'Vaccine Response', 'Infection Response', 'Immune Response', 'Transplantation', 'Autoimmune'). Client-side substring match.
species	string	None	Filter by species (e.g., 'Homo sapiens', 'Mus musculus'). Applied server-side.
limit	integer	None	Maximum number of studies to return (1-100, default 10)
verbose	bool	True	Progress flag.

Retrieve protein complex composition and function

dnakit.databases.intact_get_complex_details(*, complex_ac, format=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
complex_ac	string	Required	Complex AC (Complex Accession) in format 'CPX-XXXXX' (e.g., 'CPX-915', 'CPX-10081'). Get complex ACs from intact_get_interactions_by_complex search results.
format	string	None	Output format; see this operation's allowed values and provider defaults.
verbose	bool	True	Progress flag.

Retrieve an interaction network centered on a protein

dnakit.databases.intact_get_interaction_network(*, identifier=None, uniprot_id=None, protein_id=None, gene_symbol=None, gene_name=None, depth=None, limit=None, size=None, format=None, protein_name=None, protein=None, gene=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
identifier	string	None	IntAct identifier, UniProt ID, or gene name. Aliases: uniprot_id, protein_id, gene_symbol, gene_name.
uniprot_id	string	None	Alias for identifier: UniProt accession (e.g., 'P04637').
protein_id	string	None	Alias for identifier: protein identifier.
gene_symbol	string	None	Alias for identifier: gene symbol (e.g., 'BRCA1').
gene_name	string	None	Alias for identifier: gene name.
depth	integer	None	Network depth: 1 for direct interactions only, 2 for 2-hop network, etc. (default: 1)
limit	integer	None	Maximum number of interactions to return (default: 50, max: 200). Alias: size.
size	integer	None	Alias for limit. Maximum number of interactions to return (default: 50).
format	string	None	Output format; see this operation's allowed values and provider defaults.
protein_name	string	None	Alias for gene_symbol/identifier. Common protein name (e.g., MDM2, TP53).
protein	string	None	Alias for identifier. Gene symbol or protein name (e.g., 'TP53', 'BRCA1').
gene	string	None	DNAKit optional alias for gene_symbol
verbose	bool	True	Progress flag.

Retrieve interactions involving a protein or gene

dnakit.databases.intact_get_interactions(*, identifier, format=None, size=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
identifier	string	Required	IntAct identifier, UniProt ID, or gene name
format	string	None	Response format. Only 'json' is produced by this endpoint.
size	integer | null	None	Maximum number of interactions to return (default 25). IntAct entries commonly have far more -- the response reports the true total as 'hitCount', so raise 'size' to that value to retrieve them all.
verbose	bool	True	Progress flag.

Search IntAct molecular interactions by keyword

dnakit.databases.intact_search_interactions(*, query, first=None, max=None, format=None, species=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
query	string	Required	Search query string (e.g., protein name, gene name, interaction type)
first	integer	None	First result index for pagination (default: 0)
max	integer	None	Maximum number of results to return (default: 25, max: 100)
format	string	None	Output format; see this operation's allowed values and provider defaults.
species	string	None	Species name or taxonomy ID; type and supported values depend on the operation.
verbose	bool	True	Progress flag.

Retrieve protein domain and family entries

dnakit.databases.inter_pro_get_entries_for_protein(*, accession, verbose=True)

Parameter	Type	Required / default	Description and constraints
accession	string	Required	UniProt protein accession. Examples: 'P04637' (TP53, 9 entries), 'P00533' (EGFR), 'P01308' (Insulin), 'P38398' (BRCA1).
verbose	bool	True	Progress flag.

Retrieve protein domain and functional annotations

dnakit.databases.inter_pro_get_protein_domains(*, protein_id=None, accession=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
protein_id	string	None	UniProt protein ID (e.g., P05067, Q9Y6K9)
accession	string	None	DNAKit optional alias for protein_id
verbose	bool	True	Progress flag.

Search KEGG genes by keyword and organism

dnakit.databases.kegg_find_genes(*, keyword=None, organism=None, query=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
keyword	string	None	Search keyword for gene names or descriptions
organism	string	None	Organism code (e.g., 'hsa' for human, 'mmu' for mouse). Optional - searches all organisms if not specified
query	string	None	DNAKit optional alias for keyword
verbose	bool	True	Progress flag.

Retrieve KEGG gene sequences, functions and pathways

dnakit.databases.kegg_get_gene_info(*, gene_id, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_id	string	Required	KEGG gene identifier (e.g., 'hsa:348', 'hsa:3480')
verbose	bool	True	Progress flag.

Retrieve KEGG pathways containing a gene

dnakit.databases.kegg_get_gene_pathways(*, gene_id=None, gene_symbol=None, gene=None, organism=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_id	string	None	KEGG gene identifier in organism:id format. Examples: 'hsa:7157' (human TP53), 'hsa:672' (human BRCA1), 'mmu:22059' (mouse Trp53). Use organism prefix: hsa=human, mmu=mouse, rno=rat, dme=fly, sce=yeast.
gene_symbol	string	None	Alias for gene_id: human gene symbol (e.g. 'TP53', 'BRCA1'). Auto-resolved to KEGG gene ID using organism='hsa'.
gene	string	None	Alias for gene_id: human gene symbol (e.g. 'TP53', 'EGFR').
organism	string	None	KEGG organism code for gene symbol resolution (default: 'hsa' for human). Used only when gene_symbol is provided instead of gene_id.
verbose	bool	True	Progress flag.

List genes belonging to a KEGG pathway

dnakit.databases.kegg_get_pathway_genes(*, pathway_id, verbose=True)

Parameter	Type	Required / default	Description and constraints
pathway_id	string	Required	KEGG pathway identifier (e.g., 'hsa04115' for p53 signaling pathway, 'hsa04110' for cell cycle, 'hsa04210' for apoptosis). Use organism prefix: hsa=human, mmu=mouse.
verbose	bool	True	Progress flag.

Retrieve KEGG pathway genes, compounds and reactions

dnakit.databases.kegg_get_pathway_info(*, pathway_id, verbose=True)

Parameter	Type	Required / default	Description and constraints
pathway_id	string	Required	KEGG pathway identifier (e.g., 'hsa00010', 'path:hsa00010')
verbose	bool	True	Progress flag.

Search KEGG pathways by keyword

dnakit.databases.kegg_search_pathway(*, keyword, verbose=True)

Parameter	Type	Required / default	Description and constraints
keyword	string	Required	Search keyword for pathway names or descriptions (e.g., 'diabetes', 'metabolism')
verbose	bool	True	Progress flag.

Retrieve an NCBI protein record summary by identifier

dnakit.databases.ncbiprotein_get_summary(*, id, verbose=True)

Parameter	Type	Required / default	Description and constraints
id	string	Required	NCBI Protein ID (GI number or accession). Can be a single ID or comma-separated list. Examples: '119395750' (keratin 1, NP_006112), '4507879' (TP53, NP_000537), '4503747' (EGFR, NP_005219). GI numbers can be obtained from NCBI Gene genomic info or from BLAST results.
verbose	bool	True	Progress flag.

Retrieve cross-species orthologs from PANTHER

dnakit.databases.panther_ortholog(*, gene_id, organism=None, target_organism=None, ortholog_type=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_id	string	Required	Gene identifier - UniProt accession, Ensembl ID, or gene symbol. Examples: 'P04637' (TP53), 'P38398' (BRCA1).
organism	integer | null	None	Source organism NCBI taxonomy ID. Default: 9606 (human).
target_organism	integer | null	None	Target organism NCBI taxonomy ID. Default: 10090 (mouse). Others: 10116 (rat), 7227 (fly), 6239 (worm).
ortholog_type	string | null	None	Ortholog type filter. Options: 'LDO' (least diverged ortholog, default), 'O' (all orthologs), 'P' (paralogs), 'X' (xenologs), 'LDX' (least diverged xenolog), 'all' (all types).
verbose	bool	True	Progress flag.

Retrieve PDB coordinate file text

dnakit.databases.pdb_get_structure(*, pdb_id, format='cif', max_bytes=10000000, verbose=True)

Parameter	Type	Required / default	Description and constraints
pdb_id	string	Required	PDB structure identifier: four characters or pdb_ plus eight characters.
format	string	'cif'	Output format; see this operation's allowed values and provider defaults.
max_bytes	integer	10000000	Coordinate file size limit, 1–100000000 bytes.
verbose	bool	True	Progress flag.

Map PDB chains to UniProt residue intervals

dnakit.databases.pdbe_get_uniprot_mappings(*, pdb_id=None, uniprot_id=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
pdb_id	string	None	PDB identifier (4-character code). Examples: '4hhb' (hemoglobin), '1cbs' (CRABP2), '6lu7' (SARS-CoV-2 main protease).
uniprot_id	string	None	UniProt accession; do not also supply pdb_id for the reverse structure lookup.
limit	integer	None	Maximum results for the current request, not a database-wide total.
verbose	bool	True	Progress flag.

Rank protein structures by coverage and resolution

dnakit.databases.pdbe_sifts_get_best_structures(*, uniprot_accession, limit=None, offset=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
uniprot_accession	string	Required	UniProt accession for the protein. Examples: 'P04637' (TP53), 'P00533' (EGFR), 'P38398' (BRCA1), 'P01308' (Insulin).
limit	integer | null	None	Maximum number of entries to return (default 50, max 500). Proteins such as P04637 (TP53) have hundreds of structure-chain entries; raise this or use 'offset' to reach past the first page.
offset	integer | null	None	Zero-based index of the first entry to return, for paging through the ranked list (e.g. offset=50 returns entries 51-100). Default: 0.
verbose	bool	True	Progress flag.

Retrieve Pfam protein domains and residue positions

dnakit.databases.pfam_get_protein_annotations(*, accession, verbose=True)

Parameter	Type	Required / default	Description and constraints
accession	string	Required	UniProt protein accession. Examples: 'P04637' (TP53, 4 domains), 'P00533' (EGFR), 'P68431' (Histone H3.1), 'P38398' (BRCA1), 'P01308' (Insulin).
verbose	bool	True	Progress flag.

Retrieve plant pathway reactions and annotations

dnakit.databases.plant_reactome_get_pathway(*, pathway_id, verbose=True)

Parameter	Type	Required / default	Description and constraints
pathway_id	string	Required	Plant Reactome stable identifier. Format: R-{species_code}-{number}. Examples: 'R-OSA-1119312' (Photorespiration in rice), 'R-OSA-1119519' (Calvin cycle in rice).
verbose	bool	True	Progress flag.

List species covered by Plant Reactome

dnakit.databases.plant_reactome_list_species(*, verbose=True)

Parameter	Type	Required / default	Description and constraints
verbose	bool	True	Progress flag.

Search plant metabolic and regulatory pathways

dnakit.databases.plant_reactome_search_pathways(*, query, species=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
query	string	Required	Search query for plant pathways. Examples: 'photosynthesis', 'Calvin cycle', 'flavonoid biosynthesis', 'nitrogen fixation', 'auxin signaling'.
species	string | null	None	Species name to filter results. Examples: 'Oryza sativa', 'Arabidopsis thaliana', 'Zea mays'. Default: all species.
verbose	bool	True	Progress flag.

Retrieve protein sequence features and modified residues

dnakit.databases.proteins_api_get_features(*, accession, format=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
accession	string | array	Required	UniProt protein accession(s). Can be a single accession (e.g., 'P05067'), comma-separated string (e.g., 'P05067,P04637'), or list (e.g., ['P05067', 'P04637']). Use UniProt search or ebi_search_domain with domain='uniprot' to find valid accessions.
format	string	None	Response format. JSON is recommended for most use cases.
verbose	bool	True	Progress flag.

Search proteins by gene, name or accession

dnakit.databases.proteins_api_search(*, query=None, size=None, offset=None, format=None, gene_symbol=None, gene=None, reviewed=None, organism=None, taxid=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
query	string	None	Search query. Can be: gene name (e.g., 'BRCA1', 'TP53'), protein name (e.g., 'insulin', 'hemoglobin'), or UniProt accession (e.g., 'P05067'). The tool automatically determines the appropriate search parameter.
size	integer	None	Maximum number of results to return (default: 25, max: 100)
offset	integer	None	Offset for pagination (default: 0)
format	string	None	Response format. JSON is recommended for most use cases.
gene_symbol	string	None	Alias for query. Gene symbol to search (e.g., TP53, BRCA1).
gene	string	None	Alias for query. Gene name to search.
reviewed	boolean	None	If true, return only reviewed Swiss-Prot entries. If false or omitted, includes unreviewed TrEMBL entries.
organism	string	None	Restrict the search to an organism by NAME (e.g. 'Klebsiella pneumoniae', 'Escherichia coli'); use 'taxid' for numeric NCBI taxonomy ids. A purely numeric value here (e.g. '9606') is auto-corrected to a taxid lookup and the response reports it in 'normalization_note'. By default a gene/protein-name search is biased toward human (taxid 9606); set this for non-human proteins. If omitted and no human match is found, the search auto-widens to all organisms.
taxid	string	None	Restrict the search to an NCBI taxonomy id (e.g. '573' for Klebsiella pneumoniae, '562' for E. coli). Alternative to 'organism' for precise scoping.
verbose	bool	True	Progress flag.

Retrieve GO annotations and evidence for a gene product

dnakit.databases.quick_go_annotations_by_gene(*, gene_product_id, aspect=None, taxon_id=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_product_id	string	Required	Gene product identifier, typically a UniProtKB accession. Format: 'UniProtKB:P04637' (TP53), 'UniProtKB:P38398' (BRCA1), 'UniProtKB:P00533' (EGFR).
aspect	string | null	None	Filter by GO aspect: 'biological_process', 'molecular_function', or 'cellular_component'. Default: all aspects.
taxon_id	integer | null	None	Filter by NCBI taxonomy ID. Example: 9606 (human), 10090 (mouse).
limit	integer	None	Maximum number of annotations to return. Default: 25, max: 100.
verbose	bool	True	Progress flag.

Retrieve PDB experimental methods and structure metadata

dnakit.databases.rcsbdata_get_entry(*, pdb_id=None, entry_id=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
pdb_id	string	None	PDB entry ID (4 characters). Examples: '4HHB' (hemoglobin), '1TUP' (p53-DNA complex), '1M17' (EGFR kinase), '6LU7' (SARS-CoV-2 main protease).
entry_id	string	None	Alias for pdb_id (the RCSB-native term; the REST endpoint is /core/entry/{id}). Provide either pdb_id or entry_id.
verbose	bool	True	Progress flag.

Provide at least one of these parameter groups: pdb_id; entry_id.

Search Reactome pathways, reactions and entities

dnakit.databases.reactome_content_search(*, query, species=None, types=None, rows=None, start=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
query	string	Required	Search query. Examples: 'apoptosis', 'TP53', 'cell cycle', 'DNA repair', 'insulin signaling'.
species	string	None	Species name for filtering results. Default: 'Homo sapiens'. Other options: 'Mus musculus', 'Rattus norvegicus', 'Danio rerio', 'Drosophila melanogaster'.
types	string	None	Entity type to search. Options: 'Pathway', 'Reaction', 'Complex', 'Protein', 'SmallMolecule'. Default: 'Pathway'.
rows	integer | null	None	Number of results to return per page (1-1000). Omit to use Reactome's default page of 10. Queries often match far more than that ('DNA repair' in Homo sapiens matches 455 pathways), so raise this to see beyond the first page. Compare the returned 'count' against 'total_results' to know how much you are holding.
start	integer | null	None	Zero-based offset of the first result to return, for paging through large result sets. Use together with 'rows' (e.g. rows=50 with start=0, then start=50). Omit to start at the first result.
verbose	bool	True	Progress flag.

Retrieve molecules and complexes participating in a reaction

dnakit.databases.reactome_get_participants(*, stId, verbose=True)

Parameter	Type	Required / default	Description and constraints
stId	string	Required	Event Stable ID (reaction or pathway, e.g., 'R-HSA-111289'). To find reaction IDs, use Reactome_get_pathway_reactions with a pathway ID. To find pathway IDs, use Reactome_list_top_pathways.
verbose	bool	True	Progress flag.

Retrieve Reactome pathway details

dnakit.databases.reactome_get_pathway(*, stId, verbose=True)

Parameter	Type	Required / default	Description and constraints
stId	string	Required	Pathway Stable ID (e.g., 'R-HSA-73817'). To find pathway IDs, use Reactome_list_top_pathways to get top-level pathways, or Reactome_map_uniprot_to_pathways if you have a UniProt protein ID.
verbose	bool	True	Progress flag.

List reactions and subpathways within a pathway

dnakit.databases.reactome_get_pathway_reactions(*, stId, verbose=True)

Parameter	Type	Required / default	Description and constraints
stId	string	Required	Pathway Stable ID (e.g., 'R-HSA-73817'). To find pathway IDs, use Reactome_list_top_pathways to get top-level pathways, or Reactome_map_uniprot_to_pathways if you have a UniProt protein ID.
verbose	bool	True	Progress flag.

Map a UniProt protein to Reactome pathways

dnakit.databases.reactome_map_uniprot_to_pathways(*, uniprot_id=None, id=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
uniprot_id	string	None	UniProt protein accession (e.g., 'P04637' for TP53, 'P00533' for EGFR)
id	string	None	DNAKit optional alias for uniprot_id
verbose	bool	True	Progress flag.

Retrieve STRING protein functional annotations

dnakit.databases.string_get_functional_annotations(*, identifiers, species=None, category=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
identifiers	string	Required	Protein identifier (gene name or STRING ID). Examples: 'TP53', 'BRCA1', 'EGFR', '9606.ENSP00000269305'.
species	integer	None	NCBI taxonomy ID (default 9606 for human). Examples: 9606 (human), 10090 (mouse), 7227 (fly), 6239 (worm).
category	string	None	Filter by annotation category. Options: 'Process' (GO BP), 'Function' (GO MF), 'Component' (GO CC), 'KEGG', 'RCTM' (Reactome), 'WikiPathways', 'InterPro', 'Pfam', 'HPO', 'DISEASES', 'TISSUES', 'COMPARTMENTS', 'Keyword'. Leave null for all categories.
verbose	bool	True	Progress flag.

Retrieve protein interaction partners and confidence scores

dnakit.databases.string_get_interaction_partners(*, identifiers=None, species=None, limit=None, required_score=None, protein_ids=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
identifiers	string	None	Protein identifier (gene name or STRING ID). Examples: 'TP53', 'BRCA1', 'EGFR', '9606.ENSP00000269305'
species	integer	None	NCBI taxonomy ID (9606=human, 10090=mouse, 7227=fly, 6239=worm)
limit	integer	None	Maximum number of interaction partners to return
required_score	integer | null	None	Minimum combined STRING score (0-1000). 400=medium, 700=high, 900=highest confidence.
protein_ids	array | string	None	Protein identifiers; use the list or string type specified by this operation. {"items": {"type": "string"}}
verbose	bool	True	Progress flag.

Retrieve an interaction network for proteins and their neighbors

dnakit.databases.string_get_network(*, identifiers=None, species=None, limit=None, required_score=None, protein_ids=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
identifiers	string	None	Protein identifier(s). For multiple proteins, separate with '\r' (carriage return character). Examples: 'TP53', 'BRCA1\rBRCA2\rTP53', '9606.ENSP00000269305'
species	integer	None	NCBI taxonomy ID. Examples: 9606 (human), 10090 (mouse), 7227 (Drosophila), 6239 (C. elegans)
limit	integer	None	Maximum number of interaction partners to include (per protein). 0 = only interactions among input proteins.
required_score	integer | null	None	Minimum combined STRING score (0-1000). 400=medium, 700=high, 900=highest confidence. Default: 400.
protein_ids	array | string	None	Protein identifiers; use the list or string type specified by this operation. {"items": {"type": "string"}}
verbose	bool	True	Progress flag.

Test protein interaction enrichment in a protein set

dnakit.databases.string_ppi_enrichment(*, protein_ids, species=None, confidence_score=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
protein_ids	array	Required	List of protein identifiers (UniProt IDs, gene names, Ensembl IDs). Minimum 3 proteins required. {"items": {"type": "string"}, "minItems": 3}
species	integer	None	NCBI taxonomy ID (default: 9606 for human)
confidence_score	number	None	Minimum confidence score for counting interactions (0-1, default: 0.4)
verbose	bool	True	Progress flag.

Annotate residue interfaces, pockets and solvent exposure

dnakit.databases.structure_annotate_per_residue(*, operation=None, pdb_id=None, pdb_content=None, target_chain=None, partner_chains=None, ligand_resnames=None, distance_cutoff=None, core_rsa_cutoff=None, include_secondary_structure=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Operation type
pdb_id	string | null	None	4-character PDB ID (e.g. '6VJJ'). If provided, the structure is downloaded from RCSB. Exactly one of pdb_id or pdb_content must be supplied.
pdb_content	string | null	None	Raw PDB file content (string). Use when the structure is local (e.g. AlphaFold-predicted, in-memory).
target_chain	string	None	Chain ID of the protein to annotate (e.g. 'A').
partner_chains	array	None	Chain IDs that define the binding partner(s). Used to compute the interface. Empty list = no interface analysis (all dist_partner values null). {"items": {"type": "string"}, "default": []}
ligand_resnames	array	None	Three-letter residue names of bound ligands to define the ligand pocket (e.g. ['GNP', 'MG'] for GTP-analogue + magnesium). Searched across all chains. Empty list = no ligand-pocket analysis. {"items": {"type": "string"}, "default": []}
distance_cutoff	number	None	Distance cutoff in angstroms for interface and ligand-pocket classification.
core_rsa_cutoff	number	None	Relative solvent accessibility threshold below which a residue is classified as 'core'.
include_secondary_structure	boolean	None	If true and pdb_id is provided, fetch per-residue secondary structure (helix/strand/coil) from PDBe REST. Only meaningful for deposited PDB entries; ignored when pdb_content is supplied.
verbose	bool	True	Progress flag.

Extract UniProt protein variants and annotations

dnakit.databases.uni_prot_get_disease_variants_by_accession(*, accession, verbose=True)

Parameter	Type	Required / default	Description and constraints
accession	string	Required	UniProtKB accession, e.g., P05067.
verbose	bool	True	Progress flag.

Retrieve a complete UniProt entry by accession

dnakit.databases.uni_prot_get_entry_by_accession(*, accession, compact=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
accession	string	Required	UniProtKB entry accession, e.g., P05067.
compact	boolean	None	Return a bounded summary instead of the complete UniProtKB JSON entry. Defaults to true to avoid oversized LLM outputs. Set compact=false only when you explicitly need the raw UniProtKB JSON.
verbose	bool	True	Progress flag.

Extract protein domains, active sites and sequence features

dnakit.databases.uni_prot_get_features_by_accession(*, accession, verbose=True)

Parameter	Type	Required / default	Description and constraints
accession	string	Required	UniProtKB accession, e.g., 'P04637' (TP53) or 'P05067' (APP).
verbose	bool	True	Progress flag.

Extract UniProt protein function annotations

dnakit.databases.uni_prot_get_function_by_accession(*, accession, verbose=True)

Parameter	Type	Required / default	Description and constraints
accession	string	Required	UniProtKB accession, e.g., P05067.
verbose	bool	True	Progress flag.

Extract a canonical UniProt protein sequence

dnakit.databases.uni_prot_get_sequence_by_accession(*, accession, verbose=True)

Parameter	Type	Required / default	Description and constraints
accession	string	Required	UniProtKB accession, e.g., P05067.
verbose	bool	True	Progress flag.

Search UniProt proteins with structured queries

dnakit.databases.uni_prot_search(*, query, organism=None, limit=None, min_length=None, max_length=None, fields=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
query	string	Required	Search query using UniProt syntax. Simple: 'MEIOB', 'insulin'. Field searches: 'gene:TP53', 'protein_name:insulin', 'taxonomy_id:9606', 'reviewed:true'. Ranges: 'length:[100 TO 500]', 'mass:[20000 TO 50000]'. Wildcards: 'gene:MEIOB*'. Boolean: 'gene:TP53 AND taxonomy_id:9606', 'tissue:brain OR tissue:liver', 'reviewed:true NOT fragment:true'. Use parentheses for grouping: '(taxonomy_id:9606 OR taxonomy_id:10090) AND gene:TP53'. Taxon scoping: use 'taxonomy_id:<taxid>' (matches the whole lineage, so strain-level entries under a species taxid are included) or 'organism_name:"..."'. A bare 'organism:' auto-converts, and 'organism_id:<taxid>' is rewritten to 'taxonomy_id:<taxid>' with a note in data.normalization_note, because organism_id matches only the exact organism node and misses strain-level entries.
organism	string	None	Optional organism filter. Use common names ('human', 'mouse', 'rat', 'yeast') or taxonomy ID ('9606'). Automatically combined with query using AND. Will not duplicate if organism is already in query.
limit	integer	None	Maximum number of results to return (default: 25, max: 500). Accepts string or integer.
min_length	integer	None	Minimum sequence length. Auto-converts to an open-ended length range query (min to unbounded).
max_length	integer	None	Maximum sequence length. Auto-converts to an open-ended length range query (unbounded to max).
fields	array	None	List of field names to return (e.g., ['accession','gene_primary','length','organism_name']). When specified, returns raw API response with requested fields. Common fields: accession, id, gene_names, gene_primary, protein_name, organism_name, organism_id, length, mass, sequence, reviewed, cc_function. See UniProt API docs for full list. Default (no fields): returns formatted response with accession, id, protein_name, gene_names, organism, length. {"items": {"type": "string"}}
verbose	bool	True	Progress flag.

Search WikiPathways by pathway title

dnakit.databases.wiki_pathways_search(*, query, organism=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
query	string	Required	Text to search, e.g., p53
organism	string	None	Optional organism filter, e.g., 'Homo sapiens'
limit	integer	None	Maximum results for the current request, not a database-wide total.
verbose	bool	True	Progress flag.