skills.rest
biomaps-infra
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db-pubchem

Query PubChem via PUG-REST API for compound properties and searches.

Updated Mar 13, 2026
Search Tags:#drug discovery#compounds#bioactivity#cheminformatics#chemistry#pubchem
One-click install
npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-pubchem
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: db-pubchem
Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/db-pubchem
Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-pubchem

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 without needing to directly interact with complex APIs.

Core Features & Use Cases

  • Chemical Structure Search: Find compounds by name, CID, SMILES, or InChI.
  • Property Retrieval: Get detailed molecular properties like weight, formula, and LogP.
  • Bioactivity Data: Access information on compound interactions and assay results.
  • Use Case: A medicinal chemist needs to find compounds similar to a known drug candidate. They can use this Skill to perform a similarity search and retrieve properties for the top results, accelerating drug discovery.

Quick Start

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

Frequently Asked Questions about db-pubchem

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

FAQPage Schema
How do I search PubChem for chemical compounds using SMILES or CID?▼

You can retrieve molecular properties like weight, formula, and LogP by searching PubChem using a compound name, CID, or SMILES string. This bypasses direct API interaction to instantly return specific chemical data.

Can I find similar compounds for drug discovery using a substructure search?▼

Yes, you can perform similarity and substructure searches to find compounds similar to a known drug candidate. This accelerates drug discovery by identifying related chemical structures across PubChem's database.

How do I access PubChem bioactivity data for cheminformatics applications?▼

You access PubChem bioactivity data by querying specific compounds to retrieve their interaction and assay results. This provides the necessary bioactivity information for advanced cheminformatics applications and analysis.

Does this chemical database search require Python dependencies like pandas and requests?▼

Yes, querying chemical data requires Python dependencies including pubchempy, requests, and pandas. These libraries handle the PUG-REST API queries and structure the retrieved molecular data for cheminformatics use.

What is the best way to get molecular weight and canonical SMILES for aspirin?▼

The best way to get molecular weight and canonical SMILES for aspirin is to search PubChem by compound name. This directly returns the detailed molecular properties without manual API configuration.

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