# Chembl Molecule Search

> Use this skill to search ChEMBL molecules by keyword and return a compact compound summary. Do not use it for local chemistry calculations or unsupported bulk export.

- **Type:** Skill
- **Install:** `agentstack add skill-ma-compbio-lab-skillfoundry-chembl-molecule-search`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [ma-compbio-lab](https://agentstack.voostack.com/s/ma-compbio-lab)
- **Installs:** 0
- **Category:** [AI & ML](https://agentstack.voostack.com/c/ai-and-ml)
- **Latest version:** 0.1.0
- **License:** Apache-2.0
- **Upstream author:** [ma-compbio-lab](https://github.com/ma-compbio-lab)
- **Source:** https://github.com/ma-compbio-lab/SkillFoundry/tree/main/skills/drug-discovery-and-cheminformatics/chembl-molecule-search
- **Website:** https://ma-compbio-lab.github.io/SkillFoundry/

## Install

```sh
agentstack add skill-ma-compbio-lab-skillfoundry-chembl-molecule-search
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

## Purpose
Search ChEMBL by free-text query and return compact compound summaries suitable for quick cheminformatics triage.

## When to use
- You need a ChEMBL identifier and basic compound summary for a known drug or molecule name.
- You want a lightweight compound lookup before deeper cheminformatics or screening workflows.

## When not to use
- You need local descriptor calculation or docking.
- You need bulk export of a large ChEMBL slice.
- You need offline execution.

## Inputs
- Query string
- Optional result limit and output path

## Outputs
- JSON payload with query metadata and compact molecule summaries

## Requirements
- Python 3.10+
- Network access to `www.ebi.ac.uk`

## Procedure
1. Run `python3 skills/drug-discovery-and-cheminformatics/chembl-molecule-search/scripts/search_chembl_molecules.py --query imatinib --limit 1 --out skills/drug-discovery-and-cheminformatics/chembl-molecule-search/assets/chembl_imatinib.json`.
2. Inspect `molecules` for `chembl_id`, `preferred_name`, `molecule_type`, `max_phase`, `canonical_smiles`, and selected properties.
3. Use the returned ChEMBL IDs in downstream compound-knowledge workflows when needed.

## Validation
- Command exits successfully.
- `molecules` contains at least one ChEMBL result for a known query.
- The first result has a non-empty `chembl_id` and molecule summary fields.

## Failure modes and fixes
- No hits: refine the query or use a more canonical drug name.
- Too many hits: lower `--limit` and inspect the top results manually.
- HTTP errors: retry later and keep the query simple for smoke verification.

## Safety and limits
- Knowledge lookup only.
- This skill does not perform synthesis planning, structure optimization, or wet-lab decision making.

## Example
- `python3 skills/drug-discovery-and-cheminformatics/chembl-molecule-search/scripts/search_chembl_molecules.py --query imatinib --limit 1`

## Provenance
- ChEMBL web services docs: https://www.ebi.ac.uk/chembl/api/data/docs
- ChEMBL API base path: https://www.ebi.ac.uk/chembl/api/data/

## Related skills
- `clinicaltrials-study-search`

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [ma-compbio-lab](https://github.com/ma-compbio-lab)
- **Source:** [ma-compbio-lab/SkillFoundry](https://github.com/ma-compbio-lab/SkillFoundry)
- **License:** Apache-2.0
- **Homepage:** https://ma-compbio-lab.github.io/SkillFoundry/

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-ma-compbio-lab-skillfoundry-chembl-molecule-search
- Seller: https://agentstack.voostack.com/s/ma-compbio-lab
- Browse the marketplace: https://agentstack.voostack.com/browse

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