skills.rest
Juancho032007
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pubchem-database

Search PubChem compounds and retrieve molecular properties via PUG-REST API.

Updated Aug 23, 2026
Search Tags:#drug discovery#bioactivity#molecular properties#chemical database#cheminformatics#substructure search#similarity search#PubChem API
One-click install
npx skills add https://github.com/Juancho032007/claude-scientific-skills --skill pubchem-database
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/Juancho032007/claude-scientific-skills/tree/main/scientific-databases/pubchem-database
Command: npx skills add https://github.com/Juancho032007/claude-scientific-skills --skill pubchem-database

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Manually searching and analyzing chemical compounds and their properties across PubChem's vast database (110M+ compounds, 270M+ bioactivities) is time-consuming and complex. This Skill automates programmatic access via PUG-REST API and PubChemPy, enabling rapid cheminformatics tasks like property retrieval, similarity searches, and bioactivity data mining.

Core Features & Use Cases

  • Flexible Chemical Search: Find compounds by name, CID, SMILES, InChI, or molecular formula, ensuring you can locate any chemical of interest.
  • Molecular Property Retrieval: Access essential molecular properties such as molecular weight, LogP, Topological Polar Surface Area (TPSA), and hydrogen bonding descriptors.
  • Similarity & Substructure Searches: Identify structurally related compounds or those containing specific chemical motifs, crucial for lead optimization and drug discovery.
  • Use Case: A medicinal chemist needs to find all compounds structurally similar to "aspirin," retrieve their molecular weights, and check for any known bioactivities. This skill can automate the search, property extraction, and bioactivity lookup, providing a comprehensive overview for drug development.

Quick Start

To get properties for "caffeine": import pubchempy as pcp compound = pcp.get_compounds('caffeine', 'name')[0] print(f"Molecular Formula: {compound.molecular_formula}") print(f"SMILES: {compound.canonical_smiles}")