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GeneralReasoning
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pubchem-database

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

4|Updated Feb 22, 2026
Search Tags:#bioactivity#cheminformatics#pubchem#drug-discovery#pubchempy#pug-rest
One-click install
npx skills add https://github.com/GeneralReasoning/env-skillsbench --skill pubchem-database-generalreasoning
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/GeneralReasoning/env-skillsbench/tree/main/find-topk-similiar-chemicals/environment/skills/pubchem-database
Command: npx skills add https://github.com/GeneralReasoning/env-skillsbench --skill pubchem-database-generalreasoning

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 provides programmatic access to search by name, CID, or SMILES, and retrieve properties, perform similarity/substructure searches, and access bioactivity data via PUG-REST and PubChemPy.

Core Features & Use Cases

  • Search by name, CID, or SMILES and retrieve key properties (MW, formula, XLogP, TPSA, H-bond donors/acceptors, etc.).
  • Perform similarity and substructure searches to identify related compounds and motifs.
  • Access bioactivity data and assay annotations to support target discovery and lead prioritization.
  • Use cases: in drug discovery, identify analogs of a lead compound and compare their properties and activities.

Quick Start

Run a sample query to fetch aspirin's properties and print key fields.

Frequently Asked Questions about pubchem-database

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

FAQPage Schema
How do I retrieve compound properties from PubChem using a SMILES string?▼

You can retrieve compound properties by querying PubChem via PUG-REST using PubChemPy, passing a SMILES string to fetch molecular weight, formula, XLogP, TPSA, and H-bond donor/acceptor counts.

Can I perform a substructure search in PubChem to find related chemical motifs?▼

Yes, you can perform substructure and similarity searches against PubChem via PUG-REST, allowing you to identify related compounds and chemical motifs from a query structure using batch-friendly Python scripts.

How do I access PubChem bioactivity data for drug discovery target analysis?▼

Access PubChem bioactivity data and assay annotations by querying through PUG-REST, retrieving target discovery and lead prioritization information to support cheminformatics workflows.

What's the best way to batch query PubChem for multiple compound CIDs?▼

Batch querying PubChem for multiple CIDs is handled via rate-limited, batch-friendly utilities using PubChemPy and PUG-REST, parsing and annotating compound data programmatically with Python scripts.

Does querying PubChem with PUG-REST require managing API rate limits?▼

Yes, this approach relies on rate-limited utilities via PUG-REST and PubChemPy to manage request volumes when fetching compound data, properties, and bioactivities programmatically.

Can I search PubChem by compound name instead of CID or SMILES?▼

Yes, you can search PubChem by compound name, CID, or SMILES interchangeably using PUG-REST via PubChemPy, retrieving key molecular properties and bioactivity annotations for each matched compound.

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