Does this skill provide 3D structures for docking?

Yes, the skill provides workflows to access 3D-ready structures in formats like MOL2 and SDF through ZINC's file repositories, which are optimized for docking software.

Which version of ZINC does this skill access?

The skill primarily focuses on ZINC22, the most current and comprehensive version of the database maintained by UCSF.

Can I perform similarity searches with this skill?

Yes, you can perform similarity and analog searches using SMILES strings with adjustable Tanimoto distance parameters to find chemically similar molecules.

How do I filter compounds by molecular weight or LogP?

You can use the ZINC tranche system, which encodes molecular properties like hydrogen bond donors, LogP, and molecular weight into specific codes for easy filtering.

What is the ZINC Database skill used for?

It is used to search and retrieve chemical compound data from the ZINC22 repository for applications like virtual screening, drug discovery, and lead optimization.

ZINC Database Research Agent

Name: ZINC Database Research Agent
Author: Yezez9

byYezez9

0•

Data Science & ML

Accesses the ZINC22 database of over 230 million purchasable compounds for molecular docking, virtual screening, and drug discovery.

The ZINC Database skill provides a powerful interface for researchers and computational chemists to query one of the world's largest repositories of commercially available chemical compounds. By integrating directly with the ZINC22 API and file repositories, this skill enables seamless searching via ZINC IDs or SMILES strings, advanced similarity searches for analog discovery, and access to 3D-ready structures for molecular docking studies. It is specifically designed to streamline drug discovery workflows, allowing users to explore chemical space, filter compounds by physicochemical properties using the tranche system, and identify suppliers for hit molecules.

Key Features

01Perform Tanimoto-based similarity searches for analog discovery

02Access 3D-ready molecular structures (MOL2/SDF) for docking

03Search 230M+ compounds via ZINC ID, SMILES, or supplier codes

040 GitHub stars

05Filter by physicochemical tranches including LogP, MW, and H-bond donors

06Generate random compound subsets for diverse chemical space sampling

Use Cases

01Building high-throughput virtual screening libraries for target-based drug design

02Retrieving vendor information and supplier codes for experimental validation

03Identifying purchasable analogs for lead optimization and SAR studies

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent zinc-database

For use in Claude.ai and ChatGPT

Key Features

01Perform Tanimoto-based similarity searches for analog discovery

02Access 3D-ready molecular structures (MOL2/SDF) for docking

03Search 230M+ compounds via ZINC ID, SMILES, or supplier codes

040 GitHub stars

05Filter by physicochemical tranches including LogP, MW, and H-bond donors

06Generate random compound subsets for diverse chemical space sampling

Use Cases

01Building high-throughput virtual screening libraries for target-based drug design

02Retrieving vendor information and supplier codes for experimental validation

03Identifying purchasable analogs for lead optimization and SAR studies