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pubchem-database

Query PubChem by name, CID, or SMILES for properties, similarity, substructure, and bioactivity data.

15|2|Updated Dec 17, 2025
Search Tags:#bioactivity#data-extraction#pubchem#pubchempy#substructure#similarity-search#chemical-properties
One-click install
npx skills add https://github.com/rubensliv/k-dense-ai --skill pubchem-database-rubensliv
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/rubensliv/k-dense-ai/tree/main/scientific-skills/pubchem-database
Command: npx skills add https://github.com/rubensliv/k-dense-ai --skill pubchem-database-rubensliv

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Researchers often need to quickly fetch compound properties, identifiers, and bioactivity data from PubChem without manual cross-referencing across multiple endpoints.

Core Features & Use Cases

  • Retrieve key properties such as MolecularWeight, CanonicalSMILES, InChI, XLogP, and TPSA for compounds identified by name, CID, or SMILES.
  • Perform similarity and substructure searches to discover related compounds and pharmacophores.
  • Access bioactivity data and assay summaries via PUG-REST and PUG-View, with support for batch queries and automation.

Quick Start

Query PubChem for a compound by name or CID to retrieve properties, similarity results, and bioactivity data.

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 SMILES or CID?▼

To retrieve PubChem compound properties, query the database using a compound name, CID, or SMILES string. The system returns molecular weight, CanonicalSMILES, InChI, XLogP, and TPSA data via rate-limited PUG-REST calls.

Can I perform similarity and substructure searches to find related compounds in PubChem?▼

Yes, you can perform similarity and substructure searches in PubChem to discover related compounds and pharmacophores. The tool queries PUG-REST to return structural matches based on the provided SMILES input.

What is the best way to access PubChem bioactivity data and assay summaries?▼

The best way to access PubChem bioactivity data is through automated PUG-REST and PUG-View queries. The system retrieves assay summaries and bioactivity information for small molecules, supporting batch queries for screening.

Does PubChemPy work with PUG-REST for batch queries and automation?▼

PubChemPy works with PUG-REST to support batch queries and automation. The system implements rate-limited REST calls and uses PubChemPy when available, providing fallbacks and error handling for reliable data extraction.

Why does my PubChem REST API data extraction fail or return errors?▼

PubChem REST API data extraction can fail due to rate limiting or invalid identifiers. The system implements rate-limited REST calls with error handling and fallbacks to manage request thresholds and ensure stable property retrieval.

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