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felixboehm
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pubchem-database

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

Updated Mar 10, 2026
Search Tags:#drug discovery#bioactivity#molecular properties#chemical database#cheminformatics#pubchem
One-click install
npx skills add https://github.com/felixboehm/biochem-allergy --skill pubchem-database-felixboehm
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/felixboehm/biochem-allergy/tree/main/.claude/skills/pubchem-database
Command: npx skills add https://github.com/felixboehm/biochem-allergy --skill pubchem-database-felixboehm

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 programmatic access to PubChem, the world's largest chemical database, enabling users to find and retrieve detailed information about chemical compounds and their properties.

Core Features & Use Cases

  • Chemical Structure Search: Find compounds by name, CID, SMILES, or InChI.
  • Property Retrieval: Access molecular weight, LogP, TPSA, and hundreds of other properties.
  • Similarity & Substructure Search: Discover related compounds or identify specific chemical motifs.
  • Bioactivity Data: Access assay results and biological activity information.
  • Use Case: A researcher needs to find all compounds similar to a known drug candidate and retrieve their molecular weights and LogP values for a preliminary drug-likeness assessment.

Quick Start

Use the pubchem-database skill to find the molecular weight and canonical SMILES 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 like molecular weight and LogP from PubChem for drug discovery?▼

You can retrieve molecular properties from PubChem by querying the PUG-REST API using compound identifiers like name, CID, SMILES, or InChI to access detailed molecular weight, LogP, and TPSA data.

Can I search PubChem by SMILES or InChI to find related compounds for cheminformatics?▼

PubChem database querying supports searching by SMILES or InChI to perform similarity and substructure searches, enabling you to discover related compounds and identify specific chemical motifs for cheminformatics analysis.

How do I access PubChem bioactivity data and assay results for a specific compound?▼

Accessing PubChem bioactivity data involves querying the compound by name or CID through the PUG-REST API to retrieve biological activity information and assay results for drug discovery research.

Does the pubchem-database Skill work with pandas for analyzing chemical datasets?▼

The pubchem-database Skill uses pandas as a dependency, allowing you to query PubChem via PubChemPy and PUG-REST and process the retrieved chemical properties and bioactivity datasets directly in pandas DataFrames.

What is the best way to find chemical compounds similar to a known drug candidate in PubChem?▼

The best way to find similar compounds is performing a PubChem similarity search using the known drug candidate's SMILES string to retrieve related structures and their molecular properties for preliminary drug-likeness assessment.

Are there limitations to querying PubChem via PUG-REST for large-scale chemical database searches?▼

Querying PubChem via PUG-REST is subject to API rate limits and requires network connectivity, making it suitable for targeted compound searches and property retrieval rather than bulk database downloads.

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