zinc-database

ZINC Database Skill Details

Skill Overview

The ZINC Database skill helps you access the UCSF-maintained database of over 230 million purchasable compounds, supporting structure retrieval by ZINC ID or SMILES, similarity searches, and downloading of 3D structures. It is suitable for virtual screening and drug discovery research.

Use Cases

1. Virtual screening and molecular docking

Prepare compound libraries for molecular docking studies, filter molecular structures that meet specific properties (such as drug-likeness or lead-like characteristics), and download 3D-format files for docking software. Supports filtering by properties such as LogP, molecular weight, and number of hydrogen bond donors.

2. Lead discovery and analog searching

Based on the SMILES structure of known active compounds, quickly find structurally similar analogs to expand the screening scope. Identify compounds that can be purchased from suppliers to accelerate lead optimization.

3. Compound retrieval and data acquisition

Precisely query compound information using ZINC ID, supplier codes, or SMILES to obtain structural descriptions, available suppliers, and property data. Supports batch queries and random sampling for building custom compound datasets.

Core Features

1. Multidimensional compound search

Supports exact searches by ZINC ID, structure searches by SMILES (with adjustable similarity distance thresholds), and queries by supplier codes. Returns structured data such as SMILES, supplier information, and property annotations for downstream processing.

2. Similarity search and analog discovery

Performs structural similarity searches based on SMILES using the Tanimoto distance; adjusting the distance parameter controls the similarity range. Helps researchers find purchasable molecules structurally similar to hit compounds.

3. 3D structure download and docking library preparation

Provides 3D-ready molecular structure files (MOL2, SDF formats) organized by tranche system for convenient bulk download. Supports obtaining randomized compound subsets to quickly build docking libraries.

Frequently Asked Questions

Is the ZINC database free?

Yes, ZINC is a free, open database maintained by UCSF and can be accessed by anyone via the website or API. However, note that ZINC explicitly states it does not guarantee the quality of any molecules and is not responsible for errors resulting from use of the database; users should verify compound availability and structural correctness before use.

How to search for compounds in ZINC using SMILES?

Use the API endpoint https://cartblanche22.docking.org/smiles.txt and pass the smiles parameter (URL-encoded) for the search. For exact matches use dist=0; for similarity searches set dist=1-10 (smaller values are more similar). You can specify returned fields via the output_fields parameter.

How to download 3D molecular structures from the ZINC database?

ZINC provides a file repository at https://files.docking.org/zinc22/, organizing 3D structure files by tranche. You can locate the corresponding tranche using a ZINC ID and download MOL2 or SDF format files. Alternatively, you can use the API to obtain a list of compounds and then bulk-download the corresponding files.

Can compounds in ZINC be purchased directly?

ZINC itself does not sell compounds, but it provides supplier catalog information. Each compound record includes catalogs and supplier_code fields indicating which suppliers offer the compound. Actual purchases must be made by contacting the respective suppliers, and availability and pricing should be confirmed before purchase.