Can I download chemical structure files using this skill?

Yes, the skill supports downloading compound structures in various formats, including SDF, JSON, and PNG for visualization.

What chemical identifiers does the PubChem skill support?

The skill supports a wide range of identifiers including common names, Compound IDs (CID), SMILES strings, InChI, InChIKey, and molecular formulas.

Can I use this skill to perform structural similarity searches?

Yes, it allows you to perform structural similarity searches using Tanimoto thresholds and substructure searches to identify specific chemical motifs.

Does this skill provide biological activity data?

Absolutely. You can retrieve bioassay summaries, activity outcomes, and biological target identification for compounds across millions of screening records.

Are there rate limits for querying PubChem through this skill?

Yes, the skill is configured to respect PubChem's PUG-REST limits, which typically allow 5 requests per second and 400 requests per minute.

PubChem Database Explorer

Name: PubChem Database Explorer
Author: Yezez9

byYezez9

0•

Data Science & ML

Facilitates programmatic access to 110M+ chemical compounds and bioactivity data via the PubChem API and PubChemPy.

The PubChem Database skill empowers Claude to interact directly with the world's largest open chemical database, streamlining cheminformatics and research workflows. It provides comprehensive capabilities for searching chemical structures by name, CID, SMILES, or InChI, as well as retrieving essential molecular properties such as molecular weight, LogP, and TPSA. With built-in support for similarity and substructure searches, bioactivity assay retrieval, and chemical format conversion, this skill is indispensable for drug discovery, property analysis, and automated screening pipelines directly within the developer environment.

Key Features

01Automated retrieval of molecular properties like MW, LogP, and TPSA

02Comprehensive chemical structure search by Name, CID, SMILES, or InChI

03Direct access to biological assay summaries and bioactivity data

04Batch processing for drug-likeness screening and format conversion

05Tanimoto-based similarity and substructure search capabilities

060 GitHub stars

Use Cases

01Finding structurally similar compounds for lead optimization in medicinal chemistry

02Automating drug-likeness screening using Lipinski’s Rule of Five

03Extracting biological assay results and target data for specific compounds

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent pubchem-database

For use in Claude.ai and ChatGPT

Key Features

01Automated retrieval of molecular properties like MW, LogP, and TPSA

02Comprehensive chemical structure search by Name, CID, SMILES, or InChI

03Direct access to biological assay summaries and bioactivity data

04Batch processing for drug-likeness screening and format conversion

05Tanimoto-based similarity and substructure search capabilities

060 GitHub stars

Use Cases

01Finding structurally similar compounds for lead optimization in medicinal chemistry

02Automating drug-likeness screening using Lipinski’s Rule of Five

03Extracting biological assay results and target data for specific compounds

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent pubchem-database

For use in Claude.ai and ChatGPT