What is the ZINC database?

ZINC is a freely accessible repository of over 230 million purchasable compounds, widely used by scientists for virtual screening, ligand discovery, and chemical informatics.

Can I perform similarity searches with this skill?

Yes, you can perform analog and similarity searches by providing a SMILES string and adjusting the Tanimoto distance parameters to find structurally related molecules.

How do I retrieve 3D structures for docking?

The skill provides metadata and direct links to ZINC's file repositories (files.docking.org) where 3D-ready files in MOL2, SDF, and DB2.GZ formats are available.

Which version of ZINC does this skill use?

This skill primarily focuses on ZINC22, the most current and comprehensive version of the database, but it also acknowledges legacy versions like ZINC15 and ZINC20.

ZINC Database Integration

Name: ZINC Database Integration
Author: Zehong-Wang

byZehong-Wang

0•

Data Science & ML

Accesses the ZINC22 database to search, filter, and retrieve over 230 million purchasable chemical compounds for drug discovery.

The ZINC Database skill provides a specialized interface for Claude to interact with the ZINC22 repository, a massive collection of commercially available molecules maintained by UCSF. It enables researchers and developers to perform sophisticated chemical queries, including SMILES-based similarity searches, batch ZINC ID lookups, and property-based filtering using the tranche system. This skill is essential for streamlining early-stage drug discovery workflows, allowing for the rapid identification of structural analogs, the generation of diverse screening libraries, and the retrieval of 3D-ready molecular structures for virtual docking studies.

Key Features

01Perform Tanimoto-based similarity and analog searches for hit expansion.

020 GitHub stars

03Search over 230M purchasable compounds by ZINC ID or SMILES notation.

04Access 3D-ready structures optimized for molecular docking simulations.

05Filter molecules by properties like LogP, Molecular Weight, and H-bond donors.

06Identify chemical suppliers and specific catalog availability for compounds.

Use Cases

01Chemical space exploration: Sampling random lead-like or drug-like compound sets.

02Lead discovery and optimization: Finding structural analogs for identified hits.

03Virtual screening preparation: Generating chemical libraries for molecular docking.

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos zinc-database

For use in Claude.ai and ChatGPT

Download Skill