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alterlab-zinc-db

Retrieve ZINC compounds by ID or SMILES and expose 3D structures for docking.

58|9|Updated Mar 16, 2026
Search Tags:#search#docking#drug-discovery#virtual-screening#zinc#analogs#zinc22
One-click install
npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-zinc-db
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: alterlab-zinc-db
Source: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/databases/alterlab-zinc-db
Command: npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-zinc-db

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Access to ZINC's 230M+ purchasable compounds is essential for rapid hit discovery, lead optimization, and docking workflows; this skill centralizes search by ZINC ID or SMILES, supports similarity searches for analog exploration, and provides access to 3D-ready structures for docking.

Core Features & Use Cases

  • ZINC search by ID: Retrieve specific compounds using ZINC identifiers with optional output fields.
  • SMILES-based searches: Find compounds by chemical structure with exact or similarity-based matching.
  • Analog discovery: Identify purchasable analogs via controlled similarity thresholds.
  • 3D structures for docking: Access downloadable 3D structures (MOL2/SDF/DOCK-ready formats) for docking workflows.
  • Vendor catalogs & batch retrieval: Query across supplier catalogs and perform batch extractions for procurement.
  • Random sampling workflows: Generate diverse compound sets for benchmarking and screening.

Quick Start

Use the ZINC skill to query by a ZINC ID or SMILES string and retrieve downloadable 3D structures suitable for docking workflows.

Frequently Asked Questions about alterlab-zinc-db

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

FAQPage Schema
How do I retrieve ZINC compounds by ID or SMILES for virtual screening?▼

Retrieve ZINC compounds by querying specific ZINC identifiers or SMILES strings to access chemical structures, returning fields like zinc_id, smiles, and catalogs in TSV format for virtual screening workflows.

Can I find purchasable analogs using a SMILES string for lead discovery?▼

Find purchasable analogs by performing similarity-based searches using a SMILES string, applying controlled similarity thresholds to identify suitable chemical matches across ZINC20 and ZINC22 catalogs for lead discovery.

How do I access 3D docking-ready structures from the ZINC database?▼

Access 3D docking-ready structures by querying ZINC compounds through supported substance and smiles endpoints, retrieving downloadable MOL2 or SDF formats suitable for molecular docking workflows.

Does this ZINC search tool support random sampling for benchmarking compound sets?▼

Random sampling is supported through specific query endpoints, allowing you to generate diverse compound sets from the ZINC database for benchmarking and virtual screening preparation.

What is the best way to extract vendor catalog information from ZINC20 or ZINC22?▼

Extract vendor catalog information by utilizing the catitems query endpoints, which return supplier catalog details and tranches in TSV format for batch procurement and compound sourcing.

What are the limitations of querying ZINC compounds for analog searches?▼

Querying ZINC compounds for analog searches depends on available API endpoints and controlled similarity thresholds, meaning output fields and batch retrieval sizes are constrained by the TSV format response limits.

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