pubchem-database

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

Updated Dec 17, 2025
One-click install
npx skills add https://github.com/robotlearning123/claude-scientific-skills --skill pubchem-database-robotlearning123
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/robotlearning123/claude-scientific-skills/tree/main/scientific-skills/pubchem-database
Command: npx skills add https://github.com/robotlearning123/claude-scientific-skills --skill pubchem-database-robotlearning123

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill unit enables seamless access to PubChem's extensive chemical database, providing solutions for various chemical-related queries.

Core Features & Use Cases

  • Compound Search: Retrieve chemical compounds by name, CID, SMILES, or InChI.
  • Property Retrieval: Access molecular properties like MW, LogP, TPSA, and more.
  • Similarity Search: Find structurally related compounds for drug discovery.
  • Substructure Search: Locate specific chemical motifs in databases.
  • Bioactivity Data Access: Retrieve biological activity information for compounds.

Quick Start

Use the 'pubchem-database' skill to get the molecular weight and SMILES for compound '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 LogP and TPSA for a chemical compound?

To retrieve molecular properties, you can search chemical compounds by name, CID, SMILES, or InChI. This accesses PubChem to return molecular weight, LogP, TPSA, and other specific properties for cheminformatics applications.

Can I perform a substructure search to locate specific chemical motifs in PubChem?

Yes, you can perform a substructure search to locate specific chemical motifs in the PubChem database. It also supports similarity searches to find structurally related compounds for drug discovery workflows.

How do I access bioactivity data for compounds using the PUG-REST API?

You can access biological activity data for compounds via the PUG-REST API using PubChemPy. It retrieves biological activity information to support drug discovery and cheminformatics workflows.

Do I need PubChemPy to use this chemical database integration in my workflow?

Yes, you need the PubChemPy library installed as a required dependency. It facilitates interaction with the PUG-REST API to execute compound searches and retrieve molecular properties.

What is the best way to find structurally related compounds for drug discovery?

The best way to find structurally related compounds is using the similarity search feature. It queries the PubChem database to identify structurally related compounds tailored for drug discovery workflows.

Are there limitations when accessing PubChem for cheminformatics applications?

Accessing PubChem for cheminformatics requires the PubChemPy dependency and relies on the PUG-REST API. Operations are limited to compound searching, property retrieval, similarity searches, and bioactivity data access.