How do I install the Chembl Database skill?

Run npx skillmds@latest add ai4protein/chembl-database in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Chembl Database safe to use?

This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Chembl Database?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Chembl Database free to use?

Yes. Installing skills from SkillMD is free. This skill is licensed under Unknown.

Who published Chembl Database?

ai4protein (@ai4protein) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Chembl Database by ai4protein — Agent Skill

Name: Chembl Database
Author: ai4protein

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).

ai4protein a11b016 3 files · 25.1 KB Updated Sep 17, 2026

File contents

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

Resolve ChEMBL ID or start from SMILES.
Download → parse JSON/TSV on disk.
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Trust order: SKILL.md (hub tools & envelopes) → topic refs → references/legacy_guide.md (archived; may be outdated).

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

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

Frequently asked questions