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JosephWoodall
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zinc-database

Query ZINC catalog by ID or SMILES for similarity search and 3D structures.

1|Updated Mar 19, 2026
Search Tags:#cheminformatics#docking#smiles#virtual-screening#zinc#analog-search
One-click install
npx skills add https://github.com/JosephWoodall/noosphere --skill zinc-database-josephwoodall
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: zinc-database
Source: https://github.com/JosephWoodall/noosphere/tree/main/.agent/skills/zinc-database
Command: npx skills add https://github.com/JosephWoodall/noosphere --skill zinc-database-josephwoodall

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Access to the ZINC database for bulk compound retrieval, enabling efficient searching by ZINC ID or SMILES, similarity-based discovery, and ready-to-dock 3D structures for screening.

Core Features & Use Cases

  • ID/SMILES lookup: Retrieve exact compounds by ZINC ID or SMILES, with associated data like catalogs and tranche info.
  • Similarity and analog searches: Discover structurally related compounds to accelerate hit finding.
  • 3D structures for docking: Download MOL2/SDF/DOCK-ready files for virtual screening and docking workflows.
  • Lead discovery workflows: Support virtual screening, analog exploration, and supplier queries to streamline procurement.

Quick Start

Query ZINC22 by a ZINC ID or SMILES, or run a similarity search to obtain matching compounds and download 3D structures.

Frequently Asked Questions about zinc-database

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

FAQPage Schema
How do I search the ZINC database for compounds using a SMILES string?▼

You can search the ZINC database by submitting a SMILES string to retrieve exact compound matches, returning data such as zinc_id, smiles, catalogs, and tranche information for downstream filtering and procurement.

How do I retrieve ready-to-dock 3D structures from ZINC for virtual screening?▼

Retrieve ready-to-dock 3D structures from ZINC by querying specific ZINC IDs to download MOL2, SDF, or DOCK-ready files, directly supporting virtual screening and docking workflows.

Can I perform an analog search in ZINC to find structurally related compounds?▼

Yes, you can perform a similarity search in ZINC to discover structurally related compounds and analogs, accelerating hit finding and lead discovery workflows for drug discovery.

What data is returned when looking up a compound by ZINC ID?▼

Looking up a compound by ZINC ID returns the specific zinc_id, smiles string, associated catalogs, and tranche details, providing the necessary metadata for procurement and filtering.

Does this ZINC search tool support bulk compound retrieval for lead discovery?▼

Yes, the tool enables programmatic access to the ZINC catalog for bulk compound retrieval, supporting virtual screening, analog exploration, and supplier queries to streamline procurement.

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