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zinc-database

Retrieve and analyze ZINC22 compounds by ID, SMILES, or random sampling.

4|1|Updated Jun 18, 2025
Search Tags:#docking#drug-discovery#smiles#zinc#substances#analogs#chemical-database
One-click install
npx skills add https://github.com/HolobiomicsLab/Toolomics --skill zinc-database-holobiomicslab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: zinc-database
Source: https://github.com/HolobiomicsLab/Toolomics/tree/main/mcp_host/skills/scientific-skills/scientific-skills/zinc-database
Command: npx skills add https://github.com/HolobiomicsLab/Toolomics --skill zinc-database-holobiomicslab

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

ZINC provides a centralized, searchable catalog of purchasable chemical compounds, enabling researchers to quickly locate, filter, and retrieve molecules for docking, lead discovery, or virtual screening.

Core Features & Use Cases

  • Discover and retrieve compounds by ZINC ID or SMILES.
  • Perform similarity searches, access 3D structures for docking, and find analogs for virtual screening.
  • Use in lead discovery and structure-based drug design workflows, including bulk retrieval for library assembly.

Quick Start

Use this skill to query ZINC22 for drug-like compounds matching a SMILES string or ZINC ID and retrieve basic fields such as zinc_id, smiles, and tranche.

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 ZINC using a SMILES string?▼

To retrieve purchasable compounds from ZINC, query the ZINC22 database using a SMILES string to return matching substances in TSV format with fields like zinc_id, smiles, and tranche.

What is the best way to find chemical analogs for virtual screening?▼

Finding chemical analogs for virtual screening is done by searching the ZINC22 catalog via SMILES or ZINC ID, which retrieves similar purchasable substances and their 3D structures for docking workflows.

Can I get 3D structures from ZINC22 for structure-based docking?▼

Yes, you can get 3D structures from ZINC22 for structure-based docking by retrieving compounds via ZINC ID or SMILES, returning TSV data containing the necessary smiles and catalog information.

How do I perform random sampling of drug-like compounds in ZINC?▼

Perform random sampling of drug-like compounds in ZINC by using the random sampling API endpoint, which retrieves arbitrary subsets of the 230M+ purchasable substances for library assembly.

What fields are returned when querying ZINC22 for substances?▼

Querying ZINC22 for substances returns TSV formatted data containing fields such as zinc_id, smiles, catalogs, and tranche to identify and locate purchasable compounds.

Does ZINC support bulk retrieval for lead discovery workflows?▼

ZINC supports bulk retrieval for lead discovery workflows by allowing queries across its 230M+ compound catalog via API endpoints for substances and catitems, returning bulk TSV compound data.

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