Can I generate chemical structure images?

Yes, the skill includes capabilities to download 2D structure visualizations in PNG format directly from PubChem for any compound in the database.

What is the PubChem Database skill for Claude Code?

It is a specialized capability that allows Claude to query the PubChem database via the PUG-REST API and PubChemPy to find chemical information, properties, and structures.

Does this skill provide bioactivity data?

Yes, it can retrieve biological activity data from screening assays and provide biological target information for specific compounds.

Can I search for compounds using SMILES strings?

Yes, the skill supports searching by SMILES, chemical name, CID, InChI, and molecular formula to find specific compounds or motifs.

What are the rate limits for the PubChem API?

The API generally allows up to 5 requests per second and 400 requests per minute. The skill includes best practices to handle these limits effectively.

PubChem Database Explorer

Name: PubChem Database Explorer
Author: K-Dense-AI

byK-Dense-AI

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3,719

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Data Science & ML

Queries the PubChem database to retrieve chemical properties, perform structure searches, and access bioactivity data for over 110 million compounds.

The PubChem Database skill empowers researchers and developers to interact seamlessly with the world's largest chemical database directly within their development environment. By leveraging the PUG-REST API and PubChemPy, it facilitates comprehensive chemical structure searches by name, SMILES, or InChI, retrieves detailed molecular properties, and performs advanced similarity or substructure analyses. This skill is indispensable for cheminformatics tasks, drug discovery workflows, and any scientific project requiring high-quality, verified chemical information and bioactivity data.

Key Features

01Molecular property retrieval including weight, LogP, TPSA, and H-bond counts

02Batch processing and format conversion between SDF, JSON, and PNG

03Advanced similarity and substructure searches for chemical motif identification

04Comprehensive structure search using names, SMILES, CIDs, or InChI

05Access to bioactivity data and screening assay results

063,719 GitHub stars

Use Cases

01Automated drug-likeness screening using Lipinski's Rule of Five

02Converting chemical identifiers and generating 2D structure visualizations

03Building chemical datasets for machine learning and QSAR modeling

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add k-dense-ai/claude-scientific-skills pubchem-database

For use in Claude.ai and ChatGPT

Download Skill