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LeonChaoX
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pubchem-database

Retrieve PubChem compound properties, synonyms, and bioactivity data by identifier or structure.

783|65|Updated Feb 27, 2026
Search Tags:#drug discovery#bioactivity#molecular properties#cheminformatics#substructure search#pubchem#compound search
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill pubchem-database-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/LeonChaoX/qinyan-academic-skills/tree/main/skills/12-%E7%A7%91%E5%AD%A6%E6%95%B0%E6%8D%AE%E5%BA%93/pubchem-database
Command: npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill pubchem-database-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Chemoinformatics workflows often stall when you need fast, reliable access to chemical structures, identifiers, properties, and bioactivity records scattered across sources.

Core Features & Use Cases

  • Compound search by identifier or structure: Find compounds by name, CID, SMILES, InChI, or molecular formula, then retrieve canonical identifiers.
  • Property retrieval for analysis: Pull core molecular descriptors such as MW, XLogP, TPSA, H-bond counts, and more for single compounds or batches.
  • Structure-based discovery and screening: Run similarity searches and substructure searches to support candidate finding and motif-based virtual screening.
  • Bioactivity and annotation lookup: Retrieve assay summaries, active compounds by assay, and rich PUG-View annotations for downstream interpretation.
  • Format conversion and visualization: Convert identifiers and download structures/images (e.g., SDF/JSON/PNG) for reports and modeling inputs.

Quick Start

Use the pubchem-database skill to retrieve properties and bioactivity context for aspirin by starting from its CID.

Frequently Asked Questions about pubchem-database

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

FAQPage Schema
How do I retrieve PubChem compound properties using SMILES or CID?▼

Retrieve PubChem compound properties by querying the database using SMILES, CID, InChI, or name to fetch canonical identifiers and molecular descriptors like MW, XLogP, and TPSA.

Can I run substructure and similarity searches for virtual screening in PubChem?▼

Run substructure and similarity searches against PubChem to support motif-based virtual screening and identify candidate compounds for drug discovery workflows.

How do I get bioactivity and assay data for compounds from PubChem?▼

Fetch bioactivity and assay data by retrieving assay summaries, active compounds by assay, and rich PUG-View annotations from PubChem records for downstream interpretation.

Does PubChemPy support batch processing and rate-limited API usage?▼

PubChemPy supports batch processing and rate-limited API usage, enabling programmatic access to pull molecular properties and bioactivity context for multiple compounds efficiently.

What is the best way to convert chemical identifiers and download structures from PubChem?▼

Convert chemical identifiers and download structures or images in SDF, JSON, or PNG formats using PUG-REST endpoints to generate modeling inputs and report-ready files.

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