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

•

324

データサイエンスとML

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

概要

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.

主な機能

Comprehensive molecular property retrieval (MW, LogP, TPSA, H-bond counts)
Advanced chemical structure search by Name, CID, SMILES, InChI, or Formula
Automated chemical identifier conversion and 2D structure visualization
324 GitHub stars
Structural similarity and substructure search using Tanimoto metrics
Access to millions of bioactivity records and biological assay summaries

ユースケース

Screening compound libraries for drug-likeness using Lipinski's Rule of Five
Identifying structurally similar molecules for lead optimization in drug discovery
Extracting biological activity profiles for specific chemical motifs or motifs

概要

主な機能

Comprehensive molecular property retrieval (MW, LogP, TPSA, H-bond counts)
Advanced chemical structure search by Name, CID, SMILES, InChI, or Formula
Automated chemical identifier conversion and 2D structure visualization
324 GitHub stars
Structural similarity and substructure search using Tanimoto metrics
Access to millions of bioactivity records and biological assay summaries

ユースケース

Screening compound libraries for drug-likeness using Lipinski's Rule of Five
Identifying structurally similar molecules for lead optimization in drug discovery
Extracting biological activity profiles for specific chemical motifs or motifs