Pubchem Database
Gives you programmatic access to PubChem's 110M+ compound database through PUG-REST API and PubChemPy. You can search by name, CID, SMILES, or molecular formula, retrieve properties like molecular weight and LogP, and run similarity or substructure searches to find related compounds. The bioactivity endpoints let you pull screening assay data, which is useful for early stage drug discovery work. The skill includes helper scripts for batch processing and common queries. Response times can lag on similarity searches since they're asynchronous on PubChem's end, but PubChemPy handles the polling automatically. Solid option if you're doing cheminformatics work and need more than what RDKit gives you locally.
- skills.sh installs
- 288
- GitHub stars
- 33.2K
- last updated
- Aug 21, 2026
Install
$ npx -y skills add davila7/claude-code-templates --skill pubchem-database --agent claude-codeInstalls into .claude/skills of the current project.
Files
PubChem Database
Overview
PubChem is the world's largest freely available chemical database with 110M+ compounds and 270M+ bioactivities. Query chemical structures by name, CID, or SMILES, retrieve molecular properties, perform similarity and substructure searches, access bioactivity data using PUG-REST API and PubChemPy.
When to Use This Skill
This skill should be used when:
- Searching for chemical compounds by name, structure (SMILES/InChI), or molecular formula
- Retrieving molecular properties (MW, LogP, TPSA, hydrogen bonding descriptors)
- Performing similarity searches to find structurally related compounds
- Conducting substructure searches for specific chemical motifs
- Accessing bioactivity data from screening assays
- Converting between chemical identifier formats (CID, SMILES, InChI)
- Batch processing multiple compounds for drug-likeness screening or property analysis
Core Capabilities
1. Chemical Structure Search
Search for compounds using multiple identifier types:
By Chemical Name:
import pubchempy as pcp
compounds = pcp.get_compounds('aspirin', 'name')
compound = compounds[0]
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- Repository
- github.com/davila7/claude-code-templates
- Categories
- Backend & APIs, Databases
- First seen
- Jun 3, 2026
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