zinc-database

What problem does it solve?

Finding commercially available compounds for drug discovery, virtual screening, or analog searches is often fragmented and inefficient. This Skill automates access to the ZINC database, providing a unified interface to over 230 million purchasable compounds and their 3D structures, drastically reducing search time.

Core Features & Use Cases

• Compound Search: Query by ZINC ID, SMILES, or supplier codes for exact matches or similarity searches with customizable distance thresholds.
• 3D Structure Access: Download 3D-ready molecular structures in formats like MOL2 or SDF, optimized for molecular docking and virtual screening.
• Analog Discovery & Filtering: Efficiently find structurally similar compounds to a hit molecule and filter by drug-likeness properties using the tranche system.
• Use Case: Given a lead compound's SMILES, automatically search ZINC for 100 purchasable analogs with a specified similarity threshold, and prepare their 3D structures for immediate docking, streamlining lead optimization.

Quick Start

Search by SMILES for exact match (e.g., benzene)

curl "https://cartblanche22.docking.org/smiles.txt:smiles=c1ccccc1&output_fields=zinc_id,smiles"

Search for similar compounds (e.g., Ibuprofen analogs with Tanimoto distance = 3)

curl "https://cartblanche22.docking.org/smiles.txt:smiles=CC(C)Cc1ccc(cc1)C(C)C(=O)O&dist=3&output_fields=zinc_id,smiles,catalogs"