Individual skill
tooluniverse-small-molecule-discovery
Small molecule identification, characterization, and procurement — PubChem, ChEMBL, BindingDB, ADMET-AI, SwissADME, eMolecules, Enamine. Covers compound name to structure to activity to ADMET properties to commercial sourcing. Use for chemical biology, lead identification, probe selection, and the full small-molecule discovery pipeline.
plugins/tooluniverse/skills/tooluniverse-small-molecule-discovery/SKILL.md
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# 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_name` and `ChEMBL_search_molecules`; do not assume IDs from memory.
- ADMET properties: run `SwissADME_calculate_adme` or `ADMETAI_predict_*` on the actual SMILES; do not estimate logP, TPSA, or bioavailability.
- Binding affinities against a target: query `ChEMBL_search_activities` or `BindingDB_get_ligands_by_uniprot`; never cite IC50 values from memory.
- Commercial availability: check `eMolecules_search` or `Enamine_search_catalog`; do not assume availability.