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zinc-database

Search ZINC database compounds by ZINC ID or SMILES with similarity and 3D structures.

21|1|Updated Mar 19, 2026
Search Tags:#docking#smiles#virtual-screening#zinc#analogs#chemical-database
One-click install
npx skills add https://github.com/OwnLabAI/ownlab --skill zinc-database-ownlabai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: zinc-database
Source: https://github.com/OwnLabAI/ownlab/tree/main/mart/skills/scientific-skills/zinc-database
Command: npx skills add https://github.com/OwnLabAI/ownlab --skill zinc-database-ownlabai

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

ZINC provides programmatic access to a large library of purchasable compounds, enabling researchers to quickly locate relevant molecules by ZINC ID or SMILES, perform similarity searches, and obtain ready-to-dock 3D structures for docking and virtual screening.

Core Features & Use Cases

  • Search by ZINC ID to retrieve canonical data such as SMILES, catalogs, and tranche properties.
  • SMILES-based similarity searches and broad analog discovery with configurable distance thresholds.
  • Random sampling and batch retrieval for library construction and benchmarking.
  • Access to 3D-structured files (MOL2/SDF/DB2) for docking tools and downstream modeling.
  • Use cases include lead discovery, docking library preparation, and chemical space exploration.

Quick Start

Query ZINC22 by SMILES to find similar compounds and download their 3D structures for docking.

Frequently Asked Questions about zinc-database

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

FAQPage Schema
How do I find purchasable analogs for docking using a SMILES string?▼

The ZINC database enables similarity searching for purchasable compounds by submitting a SMILES string with a configurable distance threshold, returning matching analogs and their 3D structures for virtual screening.

What is virtual screening and how does ZINC support lead discovery workflows?▼

Virtual screening evaluates large chemical libraries to identify potential drug candidates, and ZINC supports this by providing programmatic access to filtered results, analogs, and ready-to-dock 3D structures for lead discovery.

Can I retrieve 3D structures like MOL2 or SDF files using a ZINC ID?▼

Yes, searching by ZINC ID retrieves canonical data including SMILES and catalogs, allowing you to download 3D-structured files like MOL2, SDF, or DB2 for use in downstream docking tools.

How do I get docking-ready compounds in bulk for library construction?▼

You can use random sampling and batch retrieval via the CartBlanche API endpoints to get docking-ready compounds in bulk, enabling efficient docking library construction and benchmarking.

Does the ZINC database API support custom output fields and distance parameters?▼

Yes, the CartBlanche API supports programmatic access with optional output_fields and distance parameters, allowing you to customize substance, smiles, and catitems retrieval for chemical space exploration.

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