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https://github.com/mims-harvard/ToolUniverse.git
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Shanghua
71 lines
2.0 KiB
Python
71 lines
2.0 KiB
Python
"""
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Examples for using BindingDB tools in ToolUniverse.
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BindingDB is a public database of measured binding affinities
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containing 3.2M measurements for 1.4M compounds and 11.4K targets.
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No authentication required.
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"""
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from tooluniverse import ToolUniverse
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def main():
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tu = ToolUniverse()
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tu.load_tools()
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print("=" * 60)
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print("BindingDB (Protein-Ligand Binding) Examples")
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print("=" * 60)
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# Example 1: Get ligands for EGFR by UniProt
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print("\n1. Get EGFR ligands (P00533) with IC50 < 1000 nM:")
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print("-" * 40)
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result = tu.tools.BindingDB_get_by_uniprot(
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operation="get_by_uniprot",
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uniprot_id="P00533",
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affinity_cutoff=1000
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)
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if result["status"] == "success":
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print(f"UniProt: {result['data']['uniprot_id']}")
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print(f"Ligands found: {result['data']['count']}")
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for lig in result["data"]["ligands"][:3]:
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print(f" - ID: {lig.get('monomerid', 'N/A')}, SMILES: {lig.get('smiles', 'N/A')[:30]}...")
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else:
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print(f"Error: {result['error']}")
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# Example 2: Get ligands by PDB structure
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print("\n2. Get ligands for PDB 1M17 (EGFR structure):")
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print("-" * 40)
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result = tu.tools.BindingDB_get_by_pdb(
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operation="get_by_pdb",
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pdb_ids="1M17",
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affinity_cutoff=100
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)
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if result["status"] == "success":
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print(f"PDB IDs: {result['data']['pdb_ids']}")
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print(f"Ligands found: {result['data']['count']}")
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else:
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print(f"Error: {result['error']}")
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# Example 3: Search by target name
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print("\n3. Search for COX-2 inhibitors:")
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print("-" * 40)
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result = tu.tools.BindingDB_get_by_target_name(
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operation="get_by_target_name",
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target_name="COX-2",
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affinity_cutoff=100
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)
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if result["status"] == "success":
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print(f"Target: {result['data']['target_name']}")
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print(f"Ligands found: {result['data']['count']}")
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else:
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print(f"Error: {result['error']}")
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if __name__ == "__main__":
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main()
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