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zinc-database

Search ZINC22 compounds by ZINC ID or SMILES and retrieve structured metadata.

15|2|Updated Dec 17, 2025
Search Tags:#api#docking#drug-discovery#smiles#virtual-screening#zinc#analog-search
One-click install
npx skills add https://github.com/rubensliv/k-dense-ai --skill zinc-database-rubensliv
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: zinc-database
Source: https://github.com/rubensliv/k-dense-ai/tree/main/scientific-skills/zinc-database
Command: npx skills add https://github.com/rubensliv/k-dense-ai --skill zinc-database-rubensliv

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Access to ZINC's massive library enables researchers to quickly locate purchasable compounds by ZINC ID or SMILES, perform similarity searches, and obtain 3D-ready structures for docking, analog discovery, and virtual screening workflows.

Core Features & Use Cases

  • Search by ZINC ID or SMILES to retrieve exact or related compounds with associated metadata.
  • Discover analogs and retrieve supplier catalogs for rapid procurement and library design.
  • Download 3D structures (MOL2/SDF/DB2.GZ) for docking and structure-based screening, and perform random sampling to explore chemical space.

Quick Start

Query ZINC22 for a compound by ZINC ID or SMILES and fetch its basic properties.

Frequently Asked Questions about zinc-database

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

FAQPage Schema
How do I search for purchasable compounds in ZINC using a SMILES string?▼

You can search for purchasable compounds in ZINC by inputting a SMILES string to retrieve exact matches and related analogs with structured metadata for downstream analysis.

Can I download 3D structures from ZINC22 for virtual screening and docking?▼

Yes, you can download 3D structures in MOL2, SDF, or DB2.GZ formats from ZINC22 for structure-based docking and virtual screening workflows.

What is the best way to find chemical analogs for drug discovery across ZINC?▼

The best way to find chemical analogs for drug discovery is performing a similarity search via ZINC ID or SMILES to retrieve related compounds and supplier catalogs for procurement.

How does ZINC handle tranche-based property filtering for virtual screening libraries?▼

ZINC handles tranche-based property data to support filtering, allowing you to configure output fields and narrow down chemical space for targeted virtual screening workflows.

Does the ZINC database API support random compound sampling to explore chemical space?▼

Yes, the ZINC database API supports random queries, enabling you to perform random sampling to explore chemical space across ZINC22 and related versions.

What limitations should I expect when querying ZINC for vendor catalog information?▼

When querying ZINC for vendor catalogs, limitations include needing specific ZINC IDs or SMILES for substance and catitems queries to retrieve accurate supplier catalog and procurement data.

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