zinc-database

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

Updated Mar 10, 2026

Search Tags:#virtual screening #drug discovery #molecular docking #compounds #cheminformatics #zinc

Ready to run

npx skills add https://github.com/Yezez9/Research-Agent --skill zinc-database-yezez9

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: zinc-database
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/zinc-database
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill zinc-database-yezez9

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

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

Core Features & Use Cases

Compound Search: Search by ZINC ID, SMILES, or supplier codes.
Similarity Searches: Find analogs of known compounds.
3D Structure Retrieval: Download 3D-ready structures for molecular docking.
Random Sampling: Obtain diverse sets of compounds for screening.
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 compound's SMILES and retrieve a list of similar, purchasable molecules.

Quick Start

Use the zinc-database skill to search for compounds similar to the SMILES '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 find purchasable compounds for virtual screening?▼

You can retrieve purchasable compounds by searching the ZINC database, which provides programmatic access to over 230 million commercially available molecules for virtual screening.

How do I search the ZINC database using a SMILES string?▼

You can search the ZINC database by providing a SMILES string to retrieve specific compounds or perform similarity searches to identify purchasable molecular analogs.

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

Yes, the ZINC database allows you to retrieve 3D-ready structures of purchasable compounds, providing the necessary molecular coordinates for molecular docking workflows.

What is the best way to find commercially available analogs of a hit compound?▼

Finding commercially available analogs involves performing a similarity search in the ZINC database using the hit compound's SMILES string to retrieve purchasable molecular variants.

How do I get a random sample of compounds for drug discovery?▼

You can sample random compound sets from the ZINC database to obtain diverse arrays of purchasable molecules for virtual screening and drug discovery workflows.

Does the ZINC database support searching by supplier codes?▼

Yes, the ZINC database supports compound searching by ZINC ID, SMILES, and supplier codes to identify purchasable molecules for cheminformatics research.