Swissmodel Tools¶
Configuration File: swissmodel_tools.json
Tool Type: Local
Tools Count: 4
This page contains all tools defined in the swissmodel_tools.json configuration file.
Available Tools¶
SwissModel_download_pdb (Type: SwissModelTool)¶
Download the actual 3D atomic coordinates (PDB format) of SWISS-MODEL Repository structures for a…
SwissModel_download_pdb tool specification
Tool Information:
Name:
SwissModel_download_pdbType:
SwissModelToolDescription: Download the actual 3D atomic coordinates (PDB format) of SWISS-MODEL Repository structures for a UniProt accession. Unlike SwissModel_get_models / SwissModel_get_summary (which return only JSON metadata and a coordinates URL), this tool fetches the real ATOM/HETATM records and returns them as text. Optional selectors: ‘sort’ (‘seqid’ = sequence identity, or ‘seqsim’ = sequence similarity) orders the bundled models; ‘provider’ restricts to ‘swissmodel’ (homology models) or ‘pdb’ (experimental structures); ‘template’ selects a specific template; ‘range’ restricts to models covering a residue range. Example: P04637 (human p53) returns ~5.5 MB of coordinates; provider=swissmodel isolates the homology model with a SWISS-MODEL TITLE header. Use the returned ‘pdb_content’ for structural analysis, visualization, or docking.
Parameters:
uniprot_id(string) (required) UniProt accession identifier. Examples: ‘P04637’ (human p53), ‘P00533’ (human EGFR).sort([‘string’, ‘null’]) (optional) Optional ordering for the bundled models. ‘seqid’ sorts by sequence identity to the template, ‘seqsim’ by sequence similarity.provider([‘string’, ‘null’]) (optional) Optional model-provider filter. ‘swissmodel’ = SWISS-MODEL homology models only; ‘pdb’ = experimental PDB structures only. Omit for all.template([‘string’, ‘null’]) (optional) Optional template filter; download only models built from this template (PDB ID, optionally with chain).range([‘string’, ‘null’]) (optional) Optional residue range filter (‘from-to’, e.g. ‘94-312’); download only models covering this range.
Example Usage:
query = {
"name": "SwissModel_download_pdb",
"arguments": {
"uniprot_id": "example_value"
}
}
result = tu.run(query)
SwissModel_get_models (Type: SwissModelTool)¶
Get protein structure models from SWISS-MODEL Repository for a UniProt accession. Returns pre-com…
SwissModel_get_models tool specification
Tool Information:
Name:
SwissModel_get_modelsType:
SwissModelToolDescription: Get protein structure models from SWISS-MODEL Repository for a UniProt accession. Returns pre-computed 3D models (homology models plus experimental PDB structures) with template information, sequence coverage, QMEAN quality scores, creation dates, a coordinates download URL, and complex partner information. Optional filters: ‘range’ returns only models covering a given residue range (e.g. ‘94-312’); ‘provider’ restricts to ‘swissmodel’ (homology models) or ‘pdb’ (experimental structures); ‘template’ restricts to a specific template. Example: P04637 (human p53) returns ~316 structures unfiltered, 218 with range=94-312; P00533 (EGFR) with provider=swissmodel isolates homology models. Up to 30 models are returned (use SwissModel_get_summary for the single best model).
Parameters:
uniprot_id(string) (required) UniProt accession identifier. Examples: ‘P04637’ (human p53), ‘P00533’ (human EGFR), ‘Q9Y6I3’ (human EPN1).range([‘string’, ‘null’]) (optional) Optional residue range filter; only models covering this range are returned. Format ‘from-to’, e.g. ‘94-312’.provider([‘string’, ‘null’]) (optional) Optional model-provider filter. ‘swissmodel’ returns only SWISS-MODEL homology models; ‘pdb’ returns only experimental PDB structures. Omit for both.template([‘string’, ‘null’]) (optional) Optional template filter; restrict results to models built from this template (PDB ID, optionally with chain, e.g. ‘2j6m.1.A’).
Example Usage:
query = {
"name": "SwissModel_get_models",
"arguments": {
"uniprot_id": "example_value"
}
}
result = tu.run(query)
SwissModel_get_models_batch (Type: SwissModelTool)¶
Batch SWISS-MODEL Repository lookup for up to 250 UniProt accessions in a single call. The single…
SwissModel_get_models_batch tool specification
Tool Information:
Name:
SwissModel_get_models_batchType:
SwissModelToolDescription: Batch SWISS-MODEL Repository lookup for up to 250 UniProt accessions in a single call. The single-accession tools (SwissModel_get_models / SwissModel_get_summary) accept only one uniprot_id, requiring N separate calls for a gene or protein list; this tool resolves a whole list at once. Pass ‘uniprot_ids’ as a list (or comma-separated string). Returns one result block per accession with sequence length, model count, and up to 30 flattened models (template, coverage, QMEAN, provider, coordinates URL). Example: [‘P04637’,’P00533’,’P38398’] returns 3 result blocks (P04637=316 structures, P00533=390, P38398=35).
Parameters:
uniprot_ids(array) (required) List of up to 250 UniProt accessions, e.g. [‘P04637’, ‘P00533’, ‘P38398’]. A comma-separated string is also accepted.
Example Usage:
query = {
"name": "SwissModel_get_models_batch",
"arguments": {
"uniprot_ids": ["item1", "item2"]
}
}
result = tu.run(query)
SwissModel_get_summary (Type: SwissModelTool)¶
Get a summary of the best available homology model from SWISS-MODEL Repository for a UniProt acce…
SwissModel_get_summary tool specification
Tool Information:
Name:
SwissModel_get_summaryType:
SwissModelToolDescription: Get a summary of the best available homology model from SWISS-MODEL Repository for a UniProt accession. Returns the model with highest sequence coverage, total model count, methods distribution, and quality metrics. Useful for quickly checking if a homology model exists for a protein of interest. Example: P04637 (human p53) has 4 models, best covers residues 12-351 (86.5% coverage).
Parameters:
uniprot_id(string) (required) UniProt accession identifier. Examples: ‘P04637’ (human p53), ‘P00533’ (human EGFR).
Example Usage:
query = {
"name": "SwissModel_get_summary",
"arguments": {
"uniprot_id": "example_value"
}
}
result = tu.run(query)