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zinc-database

Search the ZINC database by ZINC ID, SMILES, or supplier codes.

Updated Aug 27, 2026
Search Tags:#virtual screening#drug discovery#compounds#cheminformatics#zinc#database search
One-click install
npx skills add https://github.com/Rowtion/Bioclaw --skill zinc-database-rowtion
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: zinc-database
Source: https://github.com/Rowtion/Bioclaw/tree/main/scientific-skills/zinc-database
Command: npx skills add https://github.com/Rowtion/Bioclaw --skill zinc-database-rowtion

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pandas, requests, rdkit, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides programmatic access to the ZINC database, enabling researchers to efficiently search and retrieve millions of purchasable chemical compounds for virtual screening and drug discovery.

Core Features & Use Cases

  • Compound Searching: Search by ZINC ID, SMILES, or supplier codes.
  • Similarity Searches: Find analogs of known active compounds.
  • Data Retrieval: Access detailed compound properties, including 3D structures for docking.
  • Use Case: A medicinal chemist needs to find commercially available analogs of a promising hit compound. They can use this Skill to search ZINC by the hit's SMILES string and retrieve a list of similar compounds with their ZINC IDs and supplier information.

Quick Start

Use the zinc-database skill to search for compounds similar to the SMILES string 'c1ccccc1' with a distance of 3.

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 commercially available compounds using a SMILES string?▼

You can search the ZINC database for commercially available compounds by providing a SMILES string to perform a similarity search, retrieving matching structures along with their ZINC IDs and supplier information.

Can I retrieve 3D molecular structures from ZINC for docking workflows?▼

Yes, you can retrieve 3D molecular structures and detailed molecular properties from the ZINC database to support docking and drug discovery workflows.

How do I find analogs of a known active compound for lead discovery?▼

To find analogs for lead discovery, you can perform a similarity search in the ZINC database using the known compound's SMILES string to identify structurally similar purchasable compounds.

What are the available search methods for retrieving chemical compounds from ZINC?▼

Available search methods for retrieving chemical compounds from ZINC include searching by ZINC ID, SMILES strings, and supplier codes to facilitate virtual screening and analog identification.

Does this ZINC database search tool require specific cheminformatics libraries?▼

Yes, this ZINC database search tool requires specific cheminformatics libraries including rdkit, along with pandas and requests, to process molecular data and handle API interactions.

What is the best way to access over 230 million compounds for virtual screening?▼

The best way to access over 230 million compounds for virtual screening is through programmatic access to the ZINC database, enabling efficient search and retrieval of purchasable chemical compounds.

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