pubchem-database

Retrieve PubChem compounds, properties, and bioactivity via PubChemPy and PUG-REST.

1|Updated Mar 19, 2026

Search Tags:#bioactivity #cheminformatics #pubchem #pubchempy #substructure #similarity-search #pug-rest

Ready to run

npx skills add https://github.com/JosephWoodall/noosphere --skill pubchem-database-josephwoodall

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/JosephWoodall/noosphere/tree/main/.agent/skills/pubchem-database
Command: npx skills add https://github.com/JosephWoodall/noosphere --skill pubchem-database-josephwoodall

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Retrieve and analyze chemical compound data from PubChem programmatically, enabling rapid access to properties, identifiers, and bioactivity insights without manual querying.

Core Features & Use Cases

Query by name, CID, or SMILES using PubChemPy and PUG-REST to fetch compounds and identifiers
Retrieve key properties such as molecular weight, canonical SMILES, InChI, XLogP, TPSA, HBondDonorCount, HBondAcceptorCount
Perform similarity and substructure searches to discover related compounds
Access bioactivity data and annotations for pharmacological context
Batch queries and data export for downstream cheminformatics workflows

Quick Start

Query aspirin by name and print CID, molecular weight, and canonical SMILES.

Frequently Asked Questions about pubchem-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I retrieve chemical compound properties from PubChem using Python?▼

You retrieve chemical compound properties from PubChem by querying compound names, CIDs, or SMILES strings to extract molecular weight, InChI, XLogP, and TPSA data. This Python integration uses PubChemPy and PUG-REST to fetch identifiers and properties programmatically.

Can I perform similarity and substructure searches on PubChem compounds?▼

Yes, you can perform similarity and substructure searches on PubChem compounds to discover related chemical structures. This functionality enables cheminformatics and drug discovery workflows by identifying structurally similar molecules using programmatic queries.

Does PUG-REST support batch processing for PubChem data retrieval?▼

Yes, PUG-REST supports batch processing for PubChem data retrieval alongside rate-limited requests. This enables efficient bulk compound queries and data export for downstream cheminformatics workflows without manual querying.

How do I access PubChem bioactivity data and annotations programmatically?▼

You access PubChem bioactivity data and annotations programmatically through optional PUG-View integration. This provides pharmacological context for retrieved compounds, enabling researchers to gather bioactivity insights alongside standard chemical properties.

What is the best way to integrate PubChemPy with PUG-REST for cheminformatics research?▼

The best way to integrate PubChemPy with PUG-REST for cheminformatics is through a unified Python interface that handles name, CID, and SMILES queries while managing rate-limited requests. This combination streamlines compound retrieval and property extraction.

What are the limitations of using PUG-REST for PubChem queries?▼

PUG-REST queries are subject to rate limits to manage server load, requiring rate-limited requests for batch processing. Users must structure batch queries appropriately to avoid exceeding PubChem API thresholds during large-scale cheminformatics workflows.