skills.rest
m0at
m0atCOMMUNITY
Explore all skills by this author →
GitHub

pubchem-database

Query PubChem by name, CID, or SMILES to retrieve compound properties.

1|Updated Apr 4, 2026
Search Tags:#bioactivity#cheminformatics#pubchem#similarity-search#substructure-search#property-retrieval#chemical-databases
One-click install
npx skills add https://github.com/m0at/claudemd --skill pubchem-database-m0at
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/m0at/claudemd/tree/main/skills/pubchem-database
Command: npx skills add https://github.com/m0at/claudemd --skill pubchem-database-m0at

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

PubChem is a vast chemical database. This Skill enables programmatic querying of PubChem to retrieve molecular properties, bioactivity data, and annotations, accelerating cheminformatics workflows.

Core Features & Use Cases

  • Chemical structure search: Find compounds by name, CID, or SMILES.
  • Property retrieval & identifier conversion: Retrieve common properties and convert between identifiers (CID, SMILES, InChI, etc.).
  • Workflow enablement: Batch queries, similarity searches, substructure searches, and access to bioactivity data via PUG-REST and PubChemPy.

Quick Start

Query PubChem by name, CID, or SMILES to retrieve properties and perform searches.

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 using Python?▼

Retrieve molecular properties from PubChem by querying compounds via name, CID, or SMILES to extract data using a Python API wrapper and PUG-REST. This approach accelerates cheminformatics workflows by automating batch property retrieval.

What is the best way to perform a similarity search in PubChem for drug discovery?▼

Perform a PubChem similarity search by submitting structural queries like SMILES to find related compounds and extract their bioactivity data. This supports drug discovery by programmatically identifying structurally similar molecules.

Can I convert between chemical identifiers like CID and SMILES in batch?▼

Yes, you can convert between chemical identifiers like CID, SMILES, and InChI in batch. The tool handles asynchronous requests and rate limits to process large sets of compounds programmatically without timing out.

Does PubChemPy support substructure searches for complex molecules?▼

Yes, PubChemPy supports substructure searches by sending structural queries to PubChem via PUG-REST. It enables cheminformatics workflows to locate specific molecular fragments and retrieve matching compound annotations.

How do I handle rate limits when querying PubChem data programmatically?▼

Handle PubChem rate limits during programmatic queries by utilizing built-in asynchronous handling and robust error management. This ensures large batch searches and property retrievals complete reliably without hitting request limits.

Related Skills

Explore More Data & Analytics Skills→
swaruplabswaruplab

pubchem-database

Query PubChem compounds by name, CID, SMILES, or InChI and retrieve properties.

Community
Advanced
NeuroAIHubNeuroAIHub
269

pubchem-database

Query the PubChem API for chemical identifiers, properties, and bioactivity data.

Official
Advanced
Imad-OuteImad-Oute

rdkit

Analyze and modify molecular structures in cheminformatics workflows.

Community
Advanced
robotlearning123robotlearning123

pubchem-database

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

Community
Advanced