Pdbe Kb Tools#

Configuration File: pdbe_kb_tools.json Tool Type: Local Tools Count: 4

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

Available Tools#

PDBe_KB_get_interface_residues (Type: PDBe_KB_Tool)#

Get protein-protein interaction interface residues for a UniProt protein from PDBe-KB. Results ar…

PDBe_KB_get_interface_residues tool specification

Tool Information:

  • Name: PDBe_KB_get_interface_residues

  • Type: PDBe_KB_Tool

  • Description: Get protein-protein interaction interface residues for a UniProt protein from PDBe-KB. Results are independently paginated at the partner, residue, and PDB-entry levels. Inspect total/returned/truncated/next-offset fields at every level and continue until the relevant level is complete.

Parameters:

  • uniprot_accession (string) (required) UniProt accession ID for the protein. Examples: ‘P04637’ (TP53), ‘P00533’ (EGFR), ‘P38398’ (BRCA1).

  • max_partners (integer) (optional) Number of interaction partners to return from partner_offset (default 60).

  • partner_offset (integer) (optional) Zero-based interaction-partner offset.

  • residue_offset (integer) (optional) Zero-based interface-residue offset applied within every returned partner.

  • residue_limit (integer) (optional) Interface residues returned per partner (default 30, maximum 500).

  • pdb_entry_offset (integer) (optional) Zero-based PDB-entry offset applied within every returned residue.

  • pdb_entry_limit (integer) (optional) PDB entries returned per residue (default 10, maximum 500).

Example Usage:

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

PDBe_KB_get_ligand_sites (Type: PDBe_KB_Tool)#

Get ligand binding site residues for a UniProt protein from PDBe-KB, including PDB structures and…

PDBe_KB_get_ligand_sites tool specification

Tool Information:

  • Name: PDBe_KB_get_ligand_sites

  • Type: PDBe_KB_Tool

  • Description: Get ligand binding site residues for a UniProt protein from PDBe-KB, including PDB structures and ligand metadata. Results are independently paginated at the ligand, residue, and PDB-entry levels. Always inspect total/returned/truncated/next-offset fields at every level and continue until the relevant level is complete; the API does not order ligands by clinical relevance.

Parameters:

  • uniprot_accession (string) (required) UniProt accession ID for the protein. Examples: ‘P04637’ (TP53), ‘P00533’ (EGFR), ‘P38398’ (BRCA1).

  • max_ligands (integer) (optional) Number of ligand records to return from ligand_offset (default 100).

  • ligand_offset (integer) (optional) Zero-based ligand offset for the next ligand page.

  • residue_offset (integer) (optional) Zero-based binding-residue offset applied within every returned ligand.

  • residue_limit (integer) (optional) Binding residues returned per ligand (default 20, maximum 500).

  • pdb_entry_offset (integer) (optional) Zero-based PDB-entry offset applied within every returned residue.

  • pdb_entry_limit (integer) (optional) PDB entries returned per residue (default 10, maximum 500).

Example Usage:

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

PDBe_KB_get_summary_stats (Type: PDBe_KB_Tool)#

Get aggregated structural summary statistics for a UniProt protein from PDBe-KB. Returns the numb…

PDBe_KB_get_summary_stats tool specification

Tool Information:

  • Name: PDBe_KB_get_summary_stats

  • Type: PDBe_KB_Tool

  • Description: Get aggregated structural summary statistics for a UniProt protein from PDBe-KB. Returns the number of PDB structures, unique ligands, interaction partners, annotations, and similar proteins available for the protein. This is a quick way to assess structural coverage before diving into detailed data. Example: P04637 (TP53) has 296 PDB structures, 121 ligands, and 54 interaction partners.

Parameters:

  • uniprot_accession (string) (required) UniProt accession ID for the protein. Examples: ‘P04637’ (TP53), ‘P00533’ (EGFR), ‘P38398’ (BRCA1), ‘P01308’ (insulin).

Example Usage:

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

PDBe_KB_get_superposition_clusters (Type: PDBe_KB_Tool)#

Get structural superposition clusters for a UniProt protein from PDBe-KB. Segments, clusters with…

PDBe_KB_get_superposition_clusters tool specification

Tool Information:

  • Name: PDBe_KB_get_superposition_clusters

  • Type: PDBe_KB_Tool

  • Description: Get structural superposition clusters for a UniProt protein from PDBe-KB. Segments, clusters within each returned segment, and members within each returned cluster are independently paginated. Inspect total/returned/truncated/next-offset fields at each level to avoid silently missing structures.

Parameters:

  • uniprot_accession (string) (required) UniProt accession ID for the protein. Examples: ‘P04637’ (TP53), ‘P00533’ (EGFR), ‘P38398’ (BRCA1).

  • segment_offset (integer) (optional) Zero-based segment offset.

  • segment_limit (integer) (optional) Segments to return (default 10, maximum 100).

  • cluster_offset (integer) (optional) Zero-based cluster offset applied within every returned segment.

  • cluster_limit (integer) (optional) Clusters returned per segment (default 10, maximum 100).

  • member_offset (integer) (optional) Zero-based member offset applied within every returned cluster.

  • member_limit (integer) (optional) Members returned per cluster (default 20, maximum 500).

Example Usage:

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