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pubchem-database

Query PubChem for compound identifiers, properties, and bioactivity data.

6|Updated Dec 30, 2025
Search Tags:#chemistry#pubchem#drug-discovery#pubchempy#similarity-search#substructure-search#property-retrieval
One-click install
npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill pubchem-database-pur3v4d3r
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/pur3v4d3r/pur3-pkb-codebase/tree/main/.claude/skills/__scientific-skills/pubchem-database
Command: npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill pubchem-database-pur3v4d3r

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill enables researchers to programmatically access PubChem data, retrieving identifiers, molecular properties, bioactivity data, and structural information for chemical compounds.

Core Features & Use Cases

  • Identifier & property retrieval: Convert names/CIDs/SMILES/InChI to canonical identifiers and fetch properties like MW, XLogP, TPSA.
  • Similarity & substructure searches: Find related compounds and search for specific motifs.
  • Bioactivity & annotations: Retrieve assay summaries, activity data, and PUG-View annotations for deeper insights.
  • Download & formats: Obtain SDF/JSON/PNG representations and synonyms for downstream analysis.

Quick Start

Query PubChem for a compound by name, CID, or SMILES and retrieve identifiers, properties, and optional bioactivity or structural 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 molecular properties from PubChem using SMILES or CID?▼

To retrieve molecular properties from PubChem, query the database using SMILES, CID, name, or InChI inputs to fetch data like MW, XLogP, and TPSA. The Skill utilizes PubChemPy and PUG-REST APIs to return canonical identifiers and a broad property set.

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

Yes, you can perform batch similarity and substructure searches on PubChem to find related compounds and specific motifs. The Skill applies cheminformatics tasks to structural inputs, returning related compounds with rate limiting and error handling.

How do I get bioactivity data and annotations for chemical compounds in drug discovery?▼

You can get bioactivity data and annotations for chemical compounds by querying PubChem through PUG-View. The Skill retrieves assay summaries and activity data, supporting drug discovery and research workflows with batch capabilities.

Does PubChemPy support downloading SDF, JSON, and PNG structural formats?▼

Yes, PubChemPy supports downloading SDF, JSON, and PNG structural representations. The Skill obtains these downloadable formats and synonyms for downstream analysis, converting names, CIDs, SMILES, or InChI into structural data outputs.

What is the best way to convert chemical names to canonical identifiers at scale?▼

The best way to convert chemical names to canonical identifiers at scale is using batch queries via PUG-REST. This Skill handles identifier conversion across names, CIDs, SMILES, and InChI formats, returning structured data with built-in rate limiting.

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