skills.rest
sagunkayastha
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pubchem-database

Query PubChem via PUG-REST API and PubChemPy for compound properties and bioactivity data.

Updated Mar 15, 2026
Search Tags:#drug discovery#bioactivity#molecular properties#chemical database#cheminformatics#pubchem
One-click install
npx skills add https://github.com/sagunkayastha/claude_skills_collection --skill pubchem-database-sagunkayastha
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/sagunkayastha/claude_skills_collection/tree/main/scientific-databases/pubchem-database
Command: npx skills add https://github.com/sagunkayastha/claude_skills_collection --skill pubchem-database-sagunkayastha

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pubchempy, requests, pandas, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides access to PubChem, the world's largest chemical database, enabling users to search for compounds, retrieve properties, and access bioactivity data, streamlining chemical research and drug discovery.

Core Features & Use Cases

  • Compound Search: Find chemicals by name, CID, SMILES, or formula.
  • Property Retrieval: Get detailed molecular properties like weight, LogP, and TPSA.
  • Similarity & Substructure Search: Discover related compounds or identify specific chemical motifs.
  • Bioactivity Data: Access assay results and target information.
  • Use Case: A medicinal chemist needs to find compounds similar to a known drug candidate and retrieve their key drug-likeness properties to assess potential.

Quick Start

Use the pubchem-database skill to search for compounds with the name 'aspirin' and print their molecular weight.

Frequently Asked Questions about pubchem-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I query PubChem for chemical compound properties using SMILES or CID?▼

You can query PubChem for chemical compound properties by using the compound's SMILES string or CID. The Skill queries the PubChem PUG-REST API to retrieve molecular properties like weight, LogP, and TPSA for cheminformatics applications.

Can I search PubChem for similar compounds to assist with drug discovery?▼

Yes, you can search PubChem for similar compounds to assist with drug discovery. The Skill performs similarity and substructure searches to discover related compounds and retrieve their key drug-likeness properties for assessment.

How do I retrieve bioactivity data and assay results from PubChem?▼

To retrieve bioactivity data and assay results from PubChem, the Skill accesses assay results and target information via the PUG-REST API. This streamlines chemical research by providing direct access to bioactivity data for queried compounds.

Does this PubChem search tool require pandas and requests to retrieve molecular data?▼

Yes, this PubChem search tool requires pandas and requests, alongside pubchempy, to retrieve molecular data. These dependencies facilitate querying the PUG-REST API and structuring the returned chemical compound data for analysis.

What is the best way to find chemical compounds by name in a cheminformatics workflow?▼

The best way to find chemical compounds by name in a cheminformatics workflow is using a Skill that queries the PubChem database. It enables searching over 110 million compounds by name, CID, SMILES, or formula to retrieve detailed molecular properties.

Are there limitations when performing substructure searches across 110 million PubChem compounds?▼

Limitations when performing substructure searches across 110 million PubChem compounds depend on the PUG-REST API's response times and rate limits. The Skill provides access to the database but is bound by the API's operational constraints for complex cheminformatics queries.

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