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pubchem-database

Search PubChem compounds and retrieve molecular properties via Python.

Updated May 10, 2026
Search Tags:#bioactivity#chemistry#pubchem#structure analysis#chemical search#property retrieval
One-click install
npx skills add https://github.com/Imad-Oute/ResearchForge --skill pubchem-database-imad-oute
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/Imad-Oute/ResearchForge/tree/main/OpenSource-Projects/claude-scientific-skills/scientific-skills/pubchem-database
Command: npx skills add https://github.com/Imad-Oute/ResearchForge --skill pubchem-database-imad-oute

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides comprehensive access to PubChem's vast chemical database, enabling researchers and developers to search, retrieve, and analyze chemical compound data seamlessly.

Core Features & Use Cases

  • Chemical Structure Search: Find compounds by name, CID, SMILES, InChI, or formula.
  • Property Retrieval: Access molecular properties, bioactivities, and annotations.
  • Similarity & Substructure Search: Identify structurally related compounds or motifs for drug discovery or cheminformatics.
  • Use Case: A researcher can query PubChem for all compounds with molecular weight under 300 and visualize their structures for lead optimization.

Quick Start

Use the pubchem-database skill to search for the molecular weight of caffeine and retrieve its canonical SMILES string.

Frequently Asked Questions about pubchem-database

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 InChI?▼

You can search PubChem for chemical compounds by name, CID, SMILES, InChI, or molecular formula. This Skill programmatically queries the PubChem API to retrieve matching compound records and their associated structural data.

Can I retrieve molecular properties and bioactivity data from PubChem via Python?▼

Yes, you can retrieve molecular properties and bioactivity annotations from PubChem using Python. This Skill leverages the pubchempy and requests libraries to extract detailed biological and chemical data for queried compounds.

How do I find structurally similar compounds in PubChem for drug discovery?▼

You can find structurally similar compounds by performing a similarity or substructure search. This Skill identifies structurally related compounds or motifs, supporting lead optimization and cheminformatics research.

Do I need pubchempy installed to extract compound data from PubChem?▼

Yes, you need the pubchempy and requests Python libraries installed. These dependencies are required for the Skill to execute API calls and programmatically access PubChem's chemical and biological database.

What is the best way to get canonical SMILES and molecular weight for a compound like caffeine?▼

The best way to get canonical SMILES and molecular weight for caffeine is to query PubChem by compound name. This Skill extracts specific molecular properties and structural identifiers directly from the PubChem database.

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