# Explore PubChem Compounds and Bioactivity

Chemical identifiers and assay records are difficult to retrieve and compare consistently. This skill guides Claude, Codex, and Claude Code through focused PubChem queries and structured interpretation.

## Install

```bash
npx skillstore add davila7/pubchem-database
```

## Metadata

- Status: approved
- Slug: davila7-pubchem-database
- Skillstore revision: r2
- Version status: missing
- Tree hash: 9521a9c912031b6ab2fe87c7bfa03b8abe281019e57caff7fa5cb85548fd1411
- Author: davila7
- GitHub username: davila7
- License: MIT
- Repository: https://github.com/davila7/claude-code-templates/tree/main/cli-tool/components/skills/scientific/pubchem-database
- Ref: c43861a65bb95efcae259cd161c9d6f4dc7eec6f
- Supported tools: Claude, Codex, Claude Code
- Audit status: complete
- Agent install advisory: allowed
- Manual install advisory: allowed
- Artifact signature: available
- Audit attestation: unavailable
- Human verification: not\_verified
- Risk factors: network, external\_commands, filesystem
- Quality score: 80
- Quality tier: silver
- Public page: https://skillstore.pages.dev/skills/davila7-pubchem-database
- Manifest: https://skillstore.pages.dev/api/skills/davila7-pubchem-database/manifest

## Capabilities

- Search PubChem compounds by name, CID, SMILES, InChI, or molecular formula.
- Retrieve molecular properties, synonyms, structure identifiers, and annotation sections.
- Run similarity and substructure searches with result limits and thresholds.
- Query compound bioassays, assay targets, active compounds, safety data, and drug information.
- Download compound structures in SDF, JSON, or PNG formats and compare batches.

## Use Cases

- Profile a Known Compound: Resolve a compound name or CID, then collect identifiers, physicochemical properties, synonyms, and selected annotations.
- Compare Compound Collections: Retrieve consistent properties for a list of compounds and highlight missing values or likely screening constraints.
- Investigate Bioactivity Evidence: Find assays, targets, and active compound records for a target or reference compound.

## Prompt Templates

### Find a Compound

```
Find {compound} in PubChem. Return its CID, formula, molecular weight, IUPAC name, canonical SMILES, and InChIKey.
```

### Compare Properties

```
Compare {compound list} using molecular weight, XLogP, TPSA, hydrogen-bond counts, and rotatable bonds. Clearly mark unavailable values.
```

### Search Related Structures

```
Use {compound or SMILES} for a PubChem similarity search at {threshold}. Limit results to {count} and summarize key property differences.
```

### Build a Bioactivity Review

```
Investigate {target or CID}. Connect relevant assays, active compounds, targets, safety annotations, and evidence gaps while respecting PubChem rate limits.
```

## Limitations

- Requires internet access and sends queries to PubChem or PubChemPy endpoints.
- Depends on PubChem availability, rate limits, record quality, and third-party package behavior.
- Similarity and substructure searches can take time and may return large result sets.
- Results are research data and do not replace expert chemical, clinical, or safety review.

## Best Practices

- Use CIDs for repeated queries and record the identifier used for each result.
- Set thresholds and maximum record counts before similarity, substructure, or assay searches.
- Check missing fields, source annotations, and retrieval dates before drawing research conclusions.

## Anti Patterns

- Do not treat PubChem records or simple property filters as medical or safety advice.
- Do not launch unbounded searches or rapid request loops that exceed PubChem limits.
- Do not overwrite downloaded files without confirming the destination and existing content.

## Security Audit

- Audited at: 2026-07-23T15:39:03.874\+00:00
- Summary: Static detections for Markdown backticks, PubChem identifiers, and official documentation links are false positives; they do not execute commands or inspect the host system. Network calls are expected PubChem access and do not transmit credentials, but the fixed binary write can overwrite structure.png in the current directory. No prompt injection, covert exfiltration, or malicious intent was found.

## Stats

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- Downloads: 12
- Favorites: 0
- Popularity score: 0