Alphafill Tools

Configuration File: alphafill_tools.json Tool Type: Local Tools Count: 1

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

Available Tools

AlphaFill_get_transplants (Type: AlphaFillTransplantsTool)

Get the ligands, cofactors, and ions that AlphaFill transplants into a protein’s AlphaFold model,…

AlphaFill_get_transplants tool specification

Tool Information:

  • Name: AlphaFill_get_transplants

  • Type: AlphaFillTransplantsTool

  • Description: Get the ligands, cofactors, and ions that AlphaFill transplants into a protein’s AlphaFold model, by UniProt accession. AlphaFold predicts apo (ligand-free) structures; AlphaFill adds small molecules by homology to experimental PDB structures. Returns the distinct transplanted compounds (PDB chemical-component codes), how many homologous hits support each, the best local fit RMSD (lower = better), and the source PDB entries. Use to hypothesize cofactor/metal/ligand/drug binding for a protein whose only structure is an AlphaFold model. No API key required.

Parameters:

  • uniprot (string) (required) UniProt accession, e.g. ‘P00520’ (ABL1), ‘P00533’ (EGFR), ‘P24941’ (CDK2).

Example Usage:

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