Dbaasp Tools

Configuration File: dbaasp_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the dbaasp_tools.json configuration file.

Available Tools

DBAASP_get_peptide (Type: DBAASPGetPeptideTool)

Get a full DBAASP antimicrobial peptide record by numeric peptide ID. Returns the sequence, N/C-t…

DBAASP_get_peptide tool specification

Tool Information:

  • Name: DBAASP_get_peptide

  • Type: DBAASPGetPeptideTool

  • Description: Get a full DBAASP antimicrobial peptide record by numeric peptide ID. Returns the sequence, N/C-terminus modifications, structure (PDB / 3D model), per-target activity measurements (MIC values with units, medium, CFU), hemolytic/cytotoxic activity, antibiofilm activity, source genes, UniProt cross-references, SMILES, and references. Keyless DBAASP v3/v4 API (dbaasp.org).

Parameters:

  • peptideId ([‘integer’, ‘string’]) (required) DBAASP numeric peptide ID. Example: 107 (Dermaseptin S4 (1-16)[M4K], sequence ALWKTLLKKVLKAAAK). Accepts a bare integer or a ‘DBAASPR_107’-style ID (digits are extracted).

Example Usage:

query = {
    "name": "DBAASP_get_peptide",
    "arguments": {
        "peptideId": "example_value"
    }
}
result = tu.run(query)

DBAASP_search_peptides (Type: DBAASPSearchPeptidesTool)

Search/filter DBAASP antimicrobial peptides by sequence (exact/substring), peptide name, target o…

DBAASP_search_peptides tool specification

Tool Information:

  • Name: DBAASP_search_peptides

  • Type: DBAASPSearchPeptidesTool

  • Description: Search/filter DBAASP antimicrobial peptides by sequence (exact/substring), peptide name, target organism/species, target group, sequence length, synthesis type, source kingdom, UniProt xref, or DBAASP ID. Returns a paginated list of matching AMPs with a total count. Enables sequence->AMP lookup, ‘what peptides are active against organism X’, and target-organism activity surveys. Keyless DBAASP v3/v4 API (dbaasp.org); pagination is limit/offset.

Parameters:

  • sequence (string) (optional) Amino-acid sequence to match (single-letter code). Pair with sequence_option (‘full’ for exact, ‘part’ for substring). Example: ‘GLFDIVKKVVGALGSL’.

  • sequence_option (string) (optional) How to match ‘sequence’: ‘full’ (exact, default) or ‘part’ (substring). Maps to DBAASP sequence.option.

  • name (string) (optional) Peptide name substring. Example: ‘Magainin’.

  • target_species (string) (optional) Target organism / species name. Example: ‘Staphylococcus aureus’. Maps to targetSpecies.value.

  • target_group (string) (optional) Target group (e.g. ‘Gram+’, ‘Gram-‘). Maps to targetGroup.value.

  • sequence_length ([‘integer’, ‘string’]) (optional) Exact peptide length filter. Maps to sequenceLength.value.

  • synthesis_type (string) (optional) Synthesis type, e.g. ‘Ribosomal’, ‘Synthetic’. Maps to synthesisType.value.

  • kingdom (string) (optional) Source kingdom/taxonomy filter. Maps to kingdom.value.

  • uniprot (string) (optional) UniProt accession cross-reference. Maps to uniprot.value.

  • dbaasp_id ([‘integer’, ‘string’]) (optional) DBAASP numeric ID filter. Maps to id.value.

  • limit (integer) (optional) Max results to return (default 25).

  • offset (integer) (optional) Result offset for pagination (default 0).

Example Usage:

query = {
    "name": "DBAASP_search_peptides",
    "arguments": {
    }
}
result = tu.run(query)