pubchem-database

Query PubChem via PUG-REST API and PubChemPy for chemical information.

Updated Mar 10, 2026

Search Tags:#drug discovery #bioactivity #molecular properties #chemical database #cheminformatics #pubchem

Ready to run

npx skills add https://github.com/Yezez9/Research-Agent --skill pubchem-database-yezez9

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/pubchem-database
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill pubchem-database-yezez9

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, a vast chemical database, enabling users to search for compounds, retrieve molecular properties, and explore bioactivity data, streamlining chemical research and drug discovery workflows.

Core Features & Use Cases

Compound Search: Find chemicals by name, CID, SMILES, or molecular formula.
Property Retrieval: Access detailed molecular properties like molecular weight, LogP, TPSA, and more.
Similarity & Substructure Search: Discover compounds structurally related to a query or containing specific chemical motifs.
Bioactivity Data: Explore biological assay results and target information.
Use Case: A medicinal chemist needs to find compounds similar to a lead molecule and retrieve their key drug-likeness properties.

Quick Start

Use the pubchem-database skill to find the molecular weight and XLogP 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 from PubChem for drug discovery?▼

To retrieve molecular properties from PubChem, query compounds by identifiers like name, CID, or SMILES to access data such as molecular weight, LogP, and TPSA for drug discovery workflows.

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

Yes, you can search PubChem for chemical compounds using a SMILES string, molecular formula, CID, or chemical name to retrieve detailed compound information and bioactivity data.

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

Perform a substructure or similarity search by querying PubChem with a chemical motif or lead molecule to discover structurally related compounds and retrieve their drug-likeness properties.

Does this PubChem cheminformatics approach work with Python and pandas?▼

Yes, this PubChem cheminformatics approach works with Python by utilizing the pubchempy and pandas dependencies to query the PUG-REST API and structure chemical data for analysis.

What is the best way to access bioactivity data and biological assay results for cheminformatics?▼

The best way to access bioactivity data for cheminformatics is querying the PubChem database to explore biological assay results and target information for specific chemical compounds.

What limitations exist when querying the PUG-REST API for chemical data?▼

When querying the PUG-REST API for chemical data, limitations include dependency on network availability and potential query rate limits imposed by the PubChem database for large batch requests.