skills.rest
jaechang-hits
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zinc-database

Query the ZINC database REST API for chemical compounds by molecular properties and SMILES similarity.

298|27|Updated Feb 18, 2026
Search Tags:#virtual screening#drug discovery#cheminformatics#smiles#zinc#compound library
One-click install
npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill zinc-database-jaechang-hits
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: zinc-database
Source: https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/structural-biology-drug-discovery/zinc-database
Command: npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill zinc-database-jaechang-hits

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, pandas, 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 for and download commercially available chemical compounds for drug discovery and virtual screening.

Core Features & Use Cases

  • Compound Searching: Filter compounds by molecular weight, logP, and other drug-likeness properties.
  • SMILES Similarity: Find compounds similar to a query molecule.
  • Library Generation: Download curated sets of lead-like, fragment-like, or drug-like compounds for docking or screening.
  • Use Case: A medicinal chemist needs to find purchasable fragments with a molecular weight under 300 Da and a logP under 3 for fragment-based drug discovery. This Skill can quickly retrieve such a library.

Quick Start

Use the zinc-database skill to search for lead-like compounds with a molecular weight between 250 and 350 and a logP between 1 and 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 for commercially available compounds in ZINC for virtual screening?▼

To search commercially available compounds in ZINC for virtual screening, query the ZINC REST API to filter by molecular weight, logP, and purchasability criteria using Python requests and pandas for data handling.

Can I find chemical compounds similar to a query molecule using SMILES?▼

Yes, you can find chemical compounds similar to a query molecule using SMILES similarity searches by querying the ZINC REST API to retrieve and compare molecular structures based on the provided SMILES string.

What is the best way to download a curated compound library for drug discovery?▼

The best way to download a curated compound library for drug discovery is to query the ZINC REST API to retrieve curated sets of lead-like, fragment-like, or drug-like compounds directly into pandas dataframes.

Do I need Python and pandas to retrieve ZINC compound information?▼

Yes, you need Python with the requests and pandas libraries to query the ZINC REST API and process the retrieved compound information effectively for cheminformatics tasks.

How do I filter ZINC compounds by fragment-likeness and molecular weight?▼

Filter ZINC compounds by fragment-likeness and molecular weight by passing specific property constraints, such as molecular weight under 300 Da and logP under 3, to the ZINC REST API to retrieve matching purchasable compounds.

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