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zinc-database

Retrieve purchasable ZINC database compounds by ID or SMILES with 3D structures for docking workflows.

48|6|Updated Mar 9, 2026
Search Tags:#docking#drug-discovery#virtual-screening#zinc#chemical-database#smiles-search
One-click install
npx skills add https://github.com/qinyan-ai/qinyan-academic-skills --skill zinc-database-qinyan-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: zinc-database
Source: https://github.com/qinyan-ai/qinyan-academic-skills/tree/main/skills/12-%E7%A7%91%E5%AD%A6%E6%95%B0%E6%8D%AE%E5%BA%93/zinc-database
Command: npx skills add https://github.com/qinyan-ai/qinyan-academic-skills --skill zinc-database-qinyan-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

ZINC is a freely accessible repository of purchasable compounds, but researchers need a streamlined way to locate, retrieve, and use those compounds in docking and screening workflows. This Skill provides direct access to ZINC22 data via ID, SMILES, and similarity queries, along with 3D-structure retrieval for docking and analog discovery.

Core Features & Use Cases

  • Search by ZINC ID or SMILES to retrieve compounds and associated metadata.
  • Perform similarity/analog searches to expand chemical space for virtual screening.
  • Download or access 3D-ready structures for docking and downstream analyses.

Quick Start

Search ZINC by a ZINC ID or SMILES and download 3D structures for docking workflows.

Frequently Asked Questions about zinc-database

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

FAQPage Schema
How do I retrieve purchasable compounds from the ZINC database for virtual screening?▼

Retrieve purchasable compounds from the ZINC database by querying specific ZINC IDs or SMILES strings. This returns essential metadata like catalogs and tranches to support your virtual screening and lead discovery workflows.

Can I download 3D structures from ZINC for docking workflows?▼

Yes, you can download 3D-ready structures directly from ZINC22 endpoints for docking workflows. Accessing these structures enables downstream molecular docking and analog discovery analyses.

How do I perform a similarity search in ZINC to find chemical analogs?▼

Perform a similarity search in ZINC by providing a SMILES string to query the database. This expands your chemical space for virtual screening by finding closely related analogs for lead discovery.

What metadata fields are available when searching ZINC by compound ID?▼

Searching ZINC by compound ID retrieves fields including zinc_id, smiles, catalogs, and tranche. This metadata helps identify purchasable compounds for targeted drug discovery workflows.

Does this ZINC search tool support both CartBlanche22 and ZINC22 endpoints?▼

Yes, the tool leverages both CartBlanche22 and ZINC22 endpoints to fetch compound data. It provides API reference documentation to guide your queries across these endpoints for drug discovery.

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