What is the PubChem Database skill?

It is a specialized capability for Claude Code that allows for seamless querying of the PubChem database using the PUG-REST API and PubChemPy library.

Can I search for compounds using SMILES strings?

Yes, the skill supports searching by chemical name, CID (Compound ID), SMILES, InChI, and molecular formula.

Does this skill provide molecular weight and LogP data?

Yes, it can retrieve comprehensive properties such as molecular weight, XLogP, TPSA, and hydrogen bond donor/acceptor counts.

Are there rate limits for PubChem queries?

Yes, to ensure stability, it is recommended to stay within 5 requests per second and 400 requests per minute as per PubChem's usage policy.

Can I perform structural similarity searches?

Yes, the skill allows you to find structurally related compounds using Tanimoto similarity thresholds and substructure matching.

PubChem Database Explorer

Name: PubChem Database Explorer
Author: x-cmd

byx-cmd

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数据科学与机器学习

Accesses and queries the world's largest chemical database for compound information, molecular properties, and bioactivity data.

The PubChem Database skill integrates the massive PubChem repository into the AI coding workflow, allowing users to search over 110 million compounds by name, CID, or SMILES string. It provides comprehensive tools for retrieving molecular properties like molecular weight and LogP, performing complex similarity or substructure searches, and accessing detailed bioactivity data. This skill is essential for cheminformatics, drug discovery, and biochemical research, enabling automated property screening and format conversion directly within the development environment.

主要功能

01Molecular property retrieval including MW, LogP, TPSA, and H-bonding

02Chemical structure search via name, CID, SMILES, or InChI

038 GitHub stars

04Automated chemical identifier conversion and structure visualization

05Advanced similarity and substructure search capabilities

06Direct access to bioactivity data from screening assays

使用场景

01Retrieving bioactivity and toxicity data for pharmaceutical analysis

02Automating drug-likeness screening using Lipinski's Rule of Five

03Building chemical identifier conversion pipelines for research datasets

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add x-cmd/skill pubchem-database

For use in Claude.ai and ChatGPT

Download Skill