Klifs Tools

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

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

Available Tools

KLIFS_get_kinase (Type: BaseRESTTool)

Get detailed information about a specific kinase from KLIFS by its kinase ID. Returns kinase name…

KLIFS_get_kinase tool specification

Tool Information:

  • Name: KLIFS_get_kinase

  • Type: BaseRESTTool

  • Description: Get detailed information about a specific kinase from KLIFS by its kinase ID. Returns kinase name, HGNC symbol, family/group classification, species, UniProt ID, IUPHAR receptor ID, and the 80-residue KLIFS kinase pocket sequence (standardized binding site residues used for structure comparison). Use KLIFS_list_kinases to find kinase IDs.

Parameters:

  • kinase_ID (integer) (required) KLIFS kinase ID (e.g., 1 for AKT1, 443 for AATK). Obtain from KLIFS_list_kinases.

Example Usage:

query = {
    "name": "KLIFS_get_kinase",
    "arguments": {
        "kinase_ID": 10
    }
}
result = tu.run(query)

KLIFS_get_ligands (Type: BaseRESTTool)

Get all ligands (co-crystallized inhibitors) bound to a specific kinase across all its crystal st…

KLIFS_get_ligands tool specification

Tool Information:

  • Name: KLIFS_get_ligands

  • Type: BaseRESTTool

  • Description: Get all ligands (co-crystallized inhibitors) bound to a specific kinase across all its crystal structures in KLIFS. Returns ligand PDB 3-letter codes, names, SMILES structures, and InChIKeys. Useful for identifying known inhibitors and their chemical scaffolds for a given kinase target. Use KLIFS_list_kinases to find kinase IDs.

Parameters:

  • kinase_ID (integer) (required) KLIFS kinase ID (e.g., 1 for AKT1). Obtain from KLIFS_list_kinases.

Example Usage:

query = {
    "name": "KLIFS_get_ligands",
    "arguments": {
        "kinase_ID": 10
    }
}
result = tu.run(query)

KLIFS_get_structures (Type: BaseRESTTool)

Get crystal structures for a specific kinase from KLIFS. Returns all annotated crystal structures…

KLIFS_get_structures tool specification

Tool Information:

  • Name: KLIFS_get_structures

  • Type: BaseRESTTool

  • Description: Get crystal structures for a specific kinase from KLIFS. Returns all annotated crystal structures with PDB IDs, ligands, DFG-in/out conformation, alpha-C helix orientation, binding site quality scores, and binding pocket fingerprints. Essential for drug discovery - identifies active vs. inactive conformations, Type I/II/III inhibitor binding sites, and DFG-in/out states. Use KLIFS_list_kinases to find kinase IDs.

Parameters:

  • kinase_ID (integer) (required) KLIFS kinase ID (e.g., 1 for AKT1). Obtain from KLIFS_list_kinases.

Example Usage:

query = {
    "name": "KLIFS_get_structures",
    "arguments": {
        "kinase_ID": 10
    }
}
result = tu.run(query)

KLIFS_get_structures_by_pdb (Type: BaseRESTTool)

Get KLIFS kinase structure data for one or more PDB entries by their PDB codes. Returns all kinas…

KLIFS_get_structures_by_pdb tool specification

Tool Information:

  • Name: KLIFS_get_structures_by_pdb

  • Type: BaseRESTTool

  • Description: Get KLIFS kinase structure data for one or more PDB entries by their PDB codes. Returns all kinase chains annotated in the specified PDB structures with DFG/alpha-C helix conformations, ligands, and pocket sequences. Useful when you have a PDB ID and want kinase-specific structural annotation.

Parameters:

  • pdb_codes (string) (required) Comma-separated list of PDB codes to look up (e.g., ‘4ekk,3mvh,1iep’). Each must be a valid 4-character PDB ID.

Example Usage:

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

KLIFS_list_kinases (Type: BaseRESTTool)

List kinases in the Kinase-Ligand Interaction Fingerprints and Structures (KLIFS) database. KLIFS…

KLIFS_list_kinases tool specification

Tool Information:

  • Name: KLIFS_list_kinases

  • Type: BaseRESTTool

  • Description: List kinases in the Kinase-Ligand Interaction Fingerprints and Structures (KLIFS) database. KLIFS contains 1,100+ kinases from 7,000+ crystal structures with curated binding pocket information. Returns kinase IDs, names, HGNC symbols, kinase family/group classification, species, and UniProt IDs. Filter by kinase group (TK, TKL, STE, CK1, AGC, CAMK, CMGC) or species (Human, Mouse, Rat).

Parameters:

  • kinase_group ([‘string’, ‘null’]) (optional) Filter by kinase group: ‘TK’ (tyrosine kinase), ‘TKL’ (TK-like), ‘STE’, ‘CK1’, ‘AGC’, ‘CAMK’, ‘CMGC’, ‘RGC’, ‘Other’

  • species ([‘string’, ‘null’]) (optional) Filter by species: ‘Human’, ‘Mouse’, ‘Rat’

Example Usage:

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