What is the ZINC database?

ZINC is a freely accessible repository of over 230 million purchasable compounds and billions of make-on-demand molecules used for virtual screening and drug discovery.

What are ZINC tranches?

Tranches are sub-groupings of compounds organized by physical properties such as molecular weight, LogP, and hydrogen bond donors to help researchers filter for drug-like or lead-like molecules.

Does this skill provide 3D structures for docking?

Yes, the skill facilitates access to 3D-ready molecular structures in formats like MOL2 and SDF via ZINC's file repositories and the CartBlanche22 interface.

Can I perform similarity searches with this skill?

Yes, you can perform similarity and analog searches by providing a SMILES string and setting a Tanimoto distance threshold via the API parameters.

Which version of ZINC does this skill focus on?

This skill primarily focuses on ZINC22, the most current and comprehensive version, while also providing context for legacy versions like ZINC15 and ZINC20.

ZINC Database Search

Name: ZINC Database Search
Author: jcafazzo

byjcafazzo

0•

Data Science & ML

Accesses and searches the ZINC22 database of 230M+ purchasable compounds for virtual screening and lead discovery.

This skill integrates Claude with the ZINC22 database, a massive repository of commercially available molecules maintained by UCSF. It enables researchers to perform chemical similarity searches using SMILES notation, look up specific compounds by ZINC ID, and retrieve 3D-ready structures for molecular docking. By providing programmatic access to various search methods and property filters (tranches), the skill streamlines the workflow for lead discovery, analog identification, and chemical space exploration directly within the development environment.

Key Features

01Query supplier codes and vendor catalogs for purchasing

02Perform Tanimoto-based similarity searches for analog discovery

03Filter compounds by 'tranches' including LogP, MW, and H-bond donors

04Retrieve 3D-ready molecular structures for docking simulations

05Search over 230 million compounds by ZINC ID or SMILES notation

060 GitHub stars

Use Cases

01Building custom virtual screening libraries for molecular docking

02Sampling diverse chemical spaces based on drug-likeness criteria

03Identifying purchasable analogs for hit-to-lead drug optimization

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add jcafazzo/thewolfondchair.ca zinc-database

For use in Claude.ai and ChatGPT

Key Features

01Query supplier codes and vendor catalogs for purchasing

02Perform Tanimoto-based similarity searches for analog discovery

03Filter compounds by 'tranches' including LogP, MW, and H-bond donors

04Retrieve 3D-ready molecular structures for docking simulations

05Search over 230 million compounds by ZINC ID or SMILES notation

060 GitHub stars

Use Cases

01Building custom virtual screening libraries for molecular docking

02Sampling diverse chemical spaces based on drug-likeness criteria

03Identifying purchasable analogs for hit-to-lead drug optimization

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add jcafazzo/thewolfondchair.ca zinc-database

For use in Claude.ai and ChatGPT