zinc-database

Query the ZINC database via CartBlanche22 API for compounds and 3D structures.

557|98|Updated Nov 7, 2025
One-click install
npx skills add https://github.com/jimmc414/Kosmos --skill zinc-database-jimmc414
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: zinc-database
Source: https://github.com/jimmc414/Kosmos/tree/main/kosmos-claude-scientific-skills/scientific-skills/zinc-database
Command: npx skills add https://github.com/jimmc414/Kosmos --skill zinc-database-jimmc414

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill provides programmatic access to the ZINC database, enabling researchers to efficiently search and retrieve information on over 230 million purchasable chemical compounds for drug discovery and virtual screening.

Core Features & Use Cases

  • Compound Search: Find molecules by ZINC ID, SMILES, or supplier codes.
  • Similarity Searches: Discover analogs based on structural similarity.
  • 3D Structure Retrieval: Access 3D-ready structures for molecular 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 compound's SMILES string and retrieve a list of similar, purchasable molecules with their ZINC IDs and supplier information.

Quick Start

Use the zinc-database skill to search for compounds similar to 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 search the ZINC database for purchasable chemical compounds by SMILES string?

To search the ZINC database for purchasable chemical compounds, query by SMILES string, ZINC ID, or supplier codes. The Skill retrieves matching molecules from over 230 million purchasable compounds using the CartBlanche22 API.

Can I retrieve 3D molecular structures from ZINC for virtual screening and drug discovery?

You can retrieve 3D-ready molecular structures from ZINC for virtual screening and drug discovery. The Skill provides programmatic access to retrieve 3D conformations needed for molecular docking workflows.

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

The best way to find commercially available analogs in ZINC is through similarity searches. Input the hit compound's SMILES string and specify a distance threshold to retrieve structurally similar purchasable molecules with their ZINC IDs and supplier information.

Does the ZINC database search tool require any external dependencies to run?

The ZINC database search tool requires no external dependencies to run. It operates independently to query the CartBlanche22 API, allowing immediate access to compound search and retrieval without prerequisite environment setup.

How many purchasable compounds can I access when searching the ZINC chemical database?

When searching the ZINC chemical database, you can access over 230 million purchasable compounds. The search covers supplier codes, ZINC IDs, and SMILES queries across this extensive compound catalog.

Can I look up a compound in ZINC using its supplier code instead of a SMILES string?

You can look up compounds in ZINC using supplier codes instead of SMILES strings. The Skill supports searching by ZINC ID, SMILES, and supplier codes to retrieve compound information from the 230 million purchasable molecule database.