tooluniverse-small-molecule-discovery
Small Molecule Discovery Skill
Systematic small molecule identification, characterization, and sourcing using PubChem, ChEMBL, BindingDB, ADMET-AI, SwissADME, eMolecules, and Enamine. Covers the full pipeline from compound name to structure, activity, ADMET properties, and commercial procurement.
Domain Reasoning
Drug-likeness is not a binary property. Lipinski's Rule of 5 was derived from orally administered, passively absorbed drugs and has many well-known exceptions: natural products, macrocycles, PROTACs, and many approved drugs violate one or more rules. The relevant question is not "does this pass Ro5?" but "does this compound's physicochemical profile match the requirements of the target, the intended route of administration, and the therapeutic context?" Focus on the specific requirements, not rigid rules.
LOOK UP DON'T GUESS
- Compound identity (CID, ChEMBL ID, SMILES): call
PubChem_get_CID_by_compound_nameandChEMBL_search_molecules; do not assume IDs from memory. - ADMET properties: run
SwissADME_calculate_admeorADMETAI_predict_*on the actual SMILES; do not estimate logP, TPSA, or bioavailability. - Binding affinities against a target: query
ChEMBL_search_activitiesorBindingDB_get_ligands_by_uniprot; never cite IC50 values from memory. - Commercial availability: check
eMolecules_searchorEnamine_search_catalog; do not assume availability.
KEY PRINCIPLES:
- Resolve identity first - Always get CID and ChEMBL ID before research
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