Are there rate limits for PubChem API queries?

Yes, PubChem suggests a maximum of 5 requests per second and 400 requests per minute to ensure stable service for all users.

Can this skill help with drug discovery workflows?

Yes, it is designed for cheminformatics tasks like similarity searches, substructure analysis, and checking drug-likeness parameters like Lipinski's rules.

What is the PubChem Database skill for Claude Code?

It is a specialized capability that allows Claude to interact with the PubChem database via PUG-REST and PubChemPy to retrieve chemical data, properties, and structures.

What identifiers can I use to search for chemicals?

You can search using chemical names, Compound IDs (CID), SMILES strings, InChI codes, InChIKeys, and molecular formulas.

Does it provide biological data?

Yes, the skill can access bioactivity data from millions of assays, including activity outcomes and biological target information.

PubChem Chemical Database

Name: PubChem Chemical Database
Author: jimmc414

byjimmc414

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324

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Data Science & ML

Interfaces with the world's largest chemical database to search, retrieve, and analyze molecular data and bioactivity.

The PubChem Database skill integrates the massive PubChem library of over 110 million compounds directly into the Claude Code environment. It enables researchers and developers to perform complex cheminformatics tasks such as structure searches via SMILES or InChI, molecular property analysis, and bioactivity screening. By leveraging the PUG-REST API and PubChemPy, it provides a powerful toolkit for drug discovery, chemical identifier conversion, and automated property retrieval, making it an essential component for autonomous scientific discovery and chemical data analysis.

Key Features

01Comprehensive molecular property retrieval (MW, LogP, TPSA, H-bond counts)

02Advanced chemical structure search by Name, CID, SMILES, InChI, or Formula

03Automated chemical identifier conversion and 2D structure visualization

04324 GitHub stars

05Structural similarity and substructure search using Tanimoto metrics

06Access to millions of bioactivity records and biological assay summaries

Use Cases

01Screening compound libraries for drug-likeness using Lipinski's Rule of Five

02Identifying structurally similar molecules for lead optimization in drug discovery

03Extracting biological activity profiles for specific chemical motifs or motifs

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add jimmc414/kosmos pubchem-database

For use in Claude.ai and ChatGPT

Download Skill