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zinc-database

Query ZINC compounds by ID or SMILES and retrieve metadata.

1|Updated Mar 11, 2026
Search Tags:#database#search#docking#smiles#zinc#analogs
One-click install
npx skills add https://github.com/SciMate-AI/scicli --skill zinc-database-scimate-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: zinc-database
Source: https://github.com/SciMate-AI/scicli/tree/main/internal/skills/bundled/claude-scientific-skills/skills/zinc-database
Command: npx skills add https://github.com/SciMate-AI/scicli --skill zinc-database-scimate-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Access to the ZINC chemical database for programmatic search, structure retrieval, and analog discovery to support virtual screening and drug discovery initiatives.

Core Features & Use Cases

  • Search by ZINC ID or SMILES for exact matches or similarity-based results
  • Retrieve 3D-ready structures and compound metadata for docking and downstream analysis
  • Explore analogs and vendor catalogs to plan procurement and screening campaigns
  • Use cases include medicinal chemists extracting purchasable compounds for lead optimization, or researchers building screening libraries

Quick Start

Run a query against ZINC22 using a SMILES string to retrieve matching compounds and essential metadata in a single step.

Frequently Asked Questions about zinc-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I search ZINC database by SMILES string for exact matches?▼

You can search the ZINC database by SMILES to retrieve exact matches and essential metadata like zinc_id, catalogs, and tranche-derived properties using a single querying step.

What is the best way to find chemical analogs in ZINC for lead optimization?▼

Finding chemical analogs in ZINC involves executing similarity-based searches using a known compound's SMILES or ZINC ID to retrieve purchasable structures for lead optimization.

Can I retrieve 3D-ready structures from ZINC22 for docking workflows?▼

Yes, ZINC22 retrieval supports obtaining 3D-ready structures and compound metadata to directly enable docking and downstream virtual screening analysis.

How do I get vendor catalog information when searching ZINC by compound ID?▼

Searching ZINC by compound ID returns specific fields including catalogs, allowing you to identify vendor information and plan procurement for screening campaigns.

Does ZINC database searching support random sampling for chemical space exploration?▼

Yes, ZINC database querying supports random sampling to help researchers explore chemical space and build diverse screening libraries for medicinal chemistry workflows.

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