# Chembl Database

> ChEMBL bioactive molecules and drugs via VenusFactory download tools. Use for molecule/drug by ID, similarity/substructure by SMILES, SAR starting points. Do NOT use for openFDA regulatory data (fda) or RDKit-only local chemistry (rdkit).

- Skill: `ai4protein/chembl-database` (Agent Skill, multi-file: 3 files)
- Install (CLI): `npx skillmds@latest add ai4protein/chembl-database`
- Raw SKILL.md: https://api.skillmd.com/api/skills/ai4protein/chembl-database/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: AI & ML
- License: Unknown
- Author: ai4protein (https://skillmd.com/u/ai4protein)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/ai4protein/chembl-database

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# ChEMBL Database

## Project Tools (VenusFactory2)

| Tool | Key args | Purpose |
|------|----------|---------|
| **download_chembl_molecule_by_id** | `mol_id`, **`out_path`** | Molecule record |
| **download_chembl_drug_by_id** | `chembl_id` / drug id, **`out_path`** | Drug record |
| **download_chembl_similarity_by_smiles** | `smiles`, threshold, **`out_path`** | Similarity neighbors |
| **download_chembl_substructure_by_smiles** | `smiles`, **`out_path`** | Substructure hits |

Returns rich JSON with `file_info`. Output path arg is **`out_path`** (not `out_dir`). Follow with `rdkit` for descriptors/filters if needed.

## Workflow

1. Resolve ChEMBL ID or start from SMILES.
2. Download → parse JSON/TSV on disk.
3. Optional RDKit property filter / figure of activity distributions.

## When NOT to use

- FDA labels / adverse events → `fda`
- Pure local fingerprinting without ChEMBL → `rdkit`

## References (progressive disclosure)

**Trust order:** `SKILL.md` (hub tools & envelopes) → topic refs → `references/legacy_guide.md` (archived; may be outdated).

```text
read_skill(skill_id="chembl_database", relative_path="references/legacy_guide.md")
```

Load legacy only after the hub workflow in this file is insufficient.