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pubchem-database

Query PubChem chemical data via PUG-REST API and PubChemPy.

8|Updated Nov 19, 2025
Search Tags:#drug discovery#bioactivity#molecular properties#chemical database#cheminformatics#pubchem
One-click install
npx skills add https://github.com/sanand0/scientific-research --skill pubchem-database-sanand0
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/sanand0/scientific-research/tree/main/.claude/skills/pubchem-database
Command: npx skills add https://github.com/sanand0/scientific-research --skill pubchem-database-sanand0

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 programmatic access to PubChem, the world's largest chemical database, enabling users to find and retrieve detailed information about millions of chemical compounds.

Core Features & Use Cases

  • Chemical Search: Find compounds by name, CID, SMILES, or molecular formula.
  • Property Retrieval: Access molecular weight, LogP, TPSA, and hundreds of other properties.
  • Structure Analysis: Perform similarity and substructure searches to find related molecules.
  • Bioactivity Data: Retrieve information on biological activities and assay results.
  • Use Case: A medicinal chemist needs to find all compounds similar to a lead compound with a Tanimoto similarity above 85% and retrieve their molecular weights and XLogP values.

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

You can retrieve molecular properties like molecular weight and LogP from PubChem by querying the PUG-REST API. The skill fetches detailed molecular properties for compounds identified by name, CID, or SMILES.

Can I search PubChem for chemical compounds using a SMILES string?▼

Yes, you can search PubChem for chemical compounds using a SMILES string. The skill supports finding compounds by various identifiers including name, CID, SMILES, and molecular formula.

How do I perform a substructure or similarity search for cheminformatics?▼

To perform substructure or similarity searches for cheminformatics, query the PubChem database via the skill. It supports finding related molecules based on structural similarity and substructure matches.

How can I access bioactivity data from PubChem for drug discovery?▼

You can access bioactivity data from PubChem for drug discovery by retrieving biological activity and assay results. The skill queries the PubChem database to fetch this information for identified compounds.

Does the pubchem-database skill work with Python and pandas?▼

Yes, the pubchem-database skill works with Python and pandas. It utilizes the pubchempy and requests libraries alongside pandas to query PubChem and structure the retrieved chemical data.

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