Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
SKILL.md
ChEMBL Database
Overview
ChEMBL is a manually curated database of bioactive molecules maintained by the European Bioinformatics Institute (EBI), containing over 2 million compounds, 19 million bioactivity measurements, 13,000+ drug targets, and data on approved drugs and clinical candidates. Access and query this data programmatically using the ChEMBL Python client for drug discovery and medicinal chemistry research.
When to Use This Skill
This skill should be used when:
Compound searches: Finding molecules by name, structure, or properties
Target information: Retrieving data about proteins, enzymes, or biological targets
Bioactivity data: Querying IC50, Ki, EC50, or other activity measurements
Drug information: Looking up approved drugs, mechanisms, or indications
Structure searches: Performing similarity or substructure searches
Cheminformatics: Analyzing molecular properties and drug-likeness
Queries execute only when data is accessed. Convert to list to force execution:
# Query is not executed yet
results = molecule.filter(pref_name__icontains='aspirin')
# Force execution
results_list = list(results)
Pagination
Results are paginated automatically. Iterate through all results:
for activity in new_client.activity.filter(target_chembl_id='CHEMBL203'):
# Process each activity
print(activity['molecule_chembl_id'])
Common Use Cases
Find Kinase Inhibitors
# Identify kinase targets
kinases = new_client.target.filter(
target_type='SINGLE PROTEIN',
pref_name__icontains='kinase'
)
# Get potent inhibitors
for kinase in kinases[:5]: # First 5 kinases
activities = new_client.activity.filter(
target_chembl_id=kinase['target_chembl_id'],
standard_type='IC50',
standard_value__lte=50
)
Explore Drug Repurposing
# Get approved drugs
drugs = new_client.drug.filter()
# For each drug, find all targets
for drug in drugs[:10]:
mechanisms = new_client.mechanism.filter(
molecule_chembl_id=drug['molecule_chembl_id']
)
