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pubchem-database

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

1|Updated Mar 12, 2026
Search Tags:#drug discovery#bioactivity#chemical database#cheminformatics#pubchem#compound search
One-click install
npx skills add https://github.com/yf8578/clawomics --skill pubchem-database-yf8578
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/yf8578/clawomics/tree/main/skills/pubchem-database
Command: npx skills add https://github.com/yf8578/clawomics --skill pubchem-database-yf8578

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 analyze bioactivity data programmatically.

Core Features & Use Cases

  • Chemical Structure Search: Find compounds by name, CID, SMILES, or molecular formula.
  • Property Retrieval: Access detailed molecular properties like molecular weight, LogP, TPSA, etc.
  • Similarity & Substructure Search: Discover related compounds or identify specific chemical motifs.
  • Bioactivity Analysis: Retrieve and summarize biological activity data for compounds.
  • Use Case: A medicinal chemist can use this Skill to find all compounds similar to a lead compound, retrieve their properties, and check their known bioactivity against specific targets.

Quick Start

Use the pubchem-database skill to find the molecular weight and canonical SMILES for aspirin.

Frequently Asked Questions about pubchem-database

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

FAQPage Schema
What is the best way to find substructure matches in a chemical database?▼

The best way to find substructure matches is using the substructure search functionality. This Skill queries PubChem to identify specific chemical motifs within compounds, facilitating structural analysis for medicinal chemistry.

How do I retrieve molecular properties like molecular weight and LogP from PubChem?▼

To retrieve molecular properties from PubChem, you can search by compound identifiers like name or CID. This Skill queries the database to fetch detailed properties including molecular weight, LogP, and TPSA for cheminformatics applications.

Can I perform a chemical structure similarity search using SMILES strings?▼

Yes, you can perform a similarity search using SMILES strings. The Skill leverages the PubChem API to discover related compounds, allowing you to identify chemical motifs and find similar structures for drug discovery.

How do I access PubChem bioactivity data for a specific compound?▼

You access PubChem bioactivity data by querying a specific compound identifier. The Skill retrieves and summarizes biological activity information, enabling you to check known target interactions for your compounds.

Does this Skill support searching compounds by molecular formula?▼

Yes, this Skill supports searching compounds by molecular formula. It uses PubChemPy and the PUG-REST API to find matching chemical structures, allowing you to retrieve comprehensive compound information using various identifiers.

What is the best way to find substructure matches in a chemical database?▼

The best way to find substructure matches is using the substructure search functionality. This Skill queries PubChem to identify specific chemical motifs within compounds, facilitating structural analysis for medicinal chemistry.

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