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pubchem-database

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

8|Updated Jan 13, 2026
Search Tags:#bioactivity#molecular properties#cheminformatics#chemistry#pubchem#compound search
One-click install
npx skills add https://github.com/hxk622/TokenDance --skill pubchem-database-hxk622
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/hxk622/TokenDance/tree/main/backend/app/skills/builtin/scientific/chemistry/pubchem-database
Command: npx skills add https://github.com/hxk622/TokenDance --skill pubchem-database-hxk622

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 access to PubChem's vast chemical database, enabling users to search for compounds, retrieve properties, and analyze bioactivity data without needing to directly interact with complex APIs.

Core Features & Use Cases

  • Compound Search: Find chemicals by name, CID, SMILES, or molecular formula.
  • Property Retrieval: Get detailed molecular properties like molecular weight, LogP, and TPSA.
  • Similarity & Substructure Search: Discover related compounds or identify specific chemical motifs.
  • Bioactivity Analysis: Access screening assay results and biological target information.
  • Use Case: A researcher needs to find all compounds similar to a known drug candidate and retrieve their key physicochemical properties for a drug-likeness assessment.

Quick Start

Use the pubchem-database skill to find compounds similar to 'aspirin' with a similarity threshold of 85%.

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 LogP and TPSA using a compound name?▼

You retrieve molecular properties like LogP and TPSA by querying the PubChem database using a chemical name, CID, SMILES, or molecular formula to return comprehensive physicochemical data for cheminformatics applications.

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

Finding compounds similar to a known drug candidate involves performing a PubChem similarity search using a chemical structure and a specified similarity threshold to identify related chemical analogs for drug discovery.

Can I access bioactivity data and biological target information through PubChem?▼

You can access bioactivity data by querying PubChem to retrieve screening assay results and biological target information directly for specified chemical compounds without needing to manually interact with complex APIs.

Does PubChemPy support substructure searches for identifying specific chemical motifs?▼

PubChemPy supports substructure searches, allowing you to query the PubChem database to discover related compounds and identify specific chemical motifs within larger molecular structures for cheminformatics analysis.

How do I convert between chemical formats for cheminformatics applications?▼

You convert between chemical formats by querying PubChem with specific identifiers like SMILES or CID, leveraging the PubChemPy and requests libraries to transform chemical structures for cheminformatics applications.

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