Pdbe Graph Tools

Configuration File: pdbe_graph_tools.json Tool Type: Local Tools Count: 5

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

Available Tools

PDBe_get_bound_molecules (Type: BaseRESTTool)

Get all bound molecules (ligands, cofactors, drugs) in a PDB structure from the PDBe Graph API. R…

PDBe_get_bound_molecules tool specification

Tool Information:

  • Name: PDBe_get_bound_molecules

  • Type: BaseRESTTool

  • Description: Get all bound molecules (ligands, cofactors, drugs) in a PDB structure from the PDBe Graph API. Returns each bound molecule group with its chemical component ID (e.g., HEM for heme, ATP for adenosine triphosphate, REA for retinoic acid), chain location, and entity information. Essential for identifying what small molecules co-crystallized with a protein. Use this to discover ligands in a structure before analyzing binding sites. Example: 4HHB returns 6 bound molecules (4 HEM groups + 2 PO4 groups); 1CBS returns REA (retinoic acid).

Parameters:

  • pdb_id (string) (required) PDB identifier (4-character code, case-insensitive). Examples: ‘4hhb’ (hemoglobin with heme), ‘1cbs’ (CRABP2 with retinoic acid), ‘6lu7’ (SARS-CoV-2 Mpro with inhibitor), ‘3hyd’ (kinase with ATP analog).

Example Usage:

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

PDBe_get_compound_details (Type: BaseRESTTool)

Get detailed chemical compound information from the PDBe Graph API by chemical component ID (3-le…

PDBe_get_compound_details tool specification

Tool Information:

  • Name: PDBe_get_compound_details

  • Type: BaseRESTTool

  • Description: Get detailed chemical compound information from the PDBe Graph API by chemical component ID (3-letter code). Returns chemical formula, molecular weight, SMILES, InChI, InChIKey, systematic names, cross-references to DrugBank/PubChem/ClinicalTrials, and stereoisomer information. More comprehensive than compound name search. Example: ‘ATP’ returns adenosine-5’-triphosphate with formula C10H16N5O13P3, weight 507.181, DrugBank DB00171, PubChem 5957.

Parameters:

  • comp_id (string) (required) Chemical component identifier (3-letter PDB ligand code, uppercase). Examples: ‘ATP’ (adenosine triphosphate), ‘HEM’ (protoporphyrin IX containing FE), ‘NAD’ (nicotinamide-adenine-dinucleotide), ‘FAD’ (flavin-adenine dinucleotide), ‘REA’ (retinoic acid).

Example Usage:

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

PDBe_get_funpdbe_annotations (Type: BaseRESTTool)

Get functional annotations from the FunPDBe consortium for a PDB structure. FunPDBe aggregates re…

PDBe_get_funpdbe_annotations tool specification

Tool Information:

  • Name: PDBe_get_funpdbe_annotations

  • Type: BaseRESTTool

  • Description: Get functional annotations from the FunPDBe consortium for a PDB structure. FunPDBe aggregates residue-level functional data from external resources including residue depth (DEPTH), dynamic cross-correlation (DynaMine), conservation scores, binding site predictions, and more. Returns per-residue annotations with confidence scores and classifications. Not all structures have FunPDBe data. Example: 4HHB returns depth annotations for all residues across chains A-D with confidence classifications (high/medium/low).

Parameters:

  • pdb_id (string) (required) PDB identifier (4-character code). Examples: ‘4hhb’ (hemoglobin, has depth annotations), ‘1cbs’ (CRABP2), ‘6lu7’ (SARS-CoV-2 main protease).

Example Usage:

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

PDBe_get_uniprot_mappings (Type: BaseRESTTool)

Get UniProt-to-PDB chain mappings for a PDB structure from the PDBe Graph API. For each UniProt a…

PDBe_get_uniprot_mappings tool specification

Tool Information:

  • Name: PDBe_get_uniprot_mappings

  • Type: BaseRESTTool

  • Description: Get UniProt-to-PDB chain mappings for a PDB structure from the PDBe Graph API. For each UniProt accession represented in the structure, returns all chain mappings with residue-level alignment (UniProt start/end, PDB start/end, identity, coverage). Essential for understanding which proteins are in a crystal structure and how they map to UniProt reference sequences. Example: 4HHB returns P69905 (HBA_HUMAN) mapped to chains A,C and P68871 (HBB_HUMAN) mapped to chains B,D.

Parameters:

  • pdb_id (string) (required) PDB identifier (4-character code). Examples: ‘4hhb’ (hemoglobin), ‘1cbs’ (CRABP2), ‘6lu7’ (SARS-CoV-2 main protease).

Example Usage:

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

PDBe_get_uniprot_structure_coverage (Type: BaseRESTTool)

Get all PDB structures mapped to a UniProt protein, ranked by quality and coverage, from the PDBe…

PDBe_get_uniprot_structure_coverage tool specification

Tool Information:

  • Name: PDBe_get_uniprot_structure_coverage

  • Type: BaseRESTTool

  • Description: Get all PDB structures mapped to a UniProt protein, ranked by quality and coverage, from the PDBe Graph API. For each structure, shows residue coverage on the UniProt sequence, resolution, experimental method, mutations present, and ligands bound. Returns the best chain per PDB entry. Essential for finding the best structural coverage for a protein of interest and identifying which regions have experimental structures vs predicted models. Example: P04637 (TP53) returns 100+ structures covering different domains (DNA-binding domain 93-292, tetramerization domain 319-360, etc.).

Parameters:

  • uniprot_id (string) (required) UniProt accession. Examples: ‘P04637’ (TP53, many structures), ‘P00533’ (EGFR), ‘P69905’ (hemoglobin alpha), ‘P01308’ (insulin).

Example Usage:

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