NATGEN

Introduction

Welcome to the NATGEN Natural Product Database. This guide provides instructions on how to use the various features of this web application.

Navigation

Use the tabs at the top of the page to navigate between different sections:

• Home: Overview of the database.
• Search: Find specific molecules using SMILES, name, or formula.
• Browse: Explore molecules dynamically loaded from the database.
• Generate: Generate 3D conformers for a given SMILES string.
• Download: Request access to download the complete database.
• User Guide: This page.
• About Us: Link to the research group website.

Searching Molecules

On the Search page, you can find molecules in three ways:

• Structure Search: Enter a valid SMILES string and click "Search".
• Name Search: Select the "Name" tab, enter a compound name, and click "Search".
• Formula Search: Select the "Formula" tab, enter a molecular formula, and click "Search".

Search results display structure, SMILES, properties, and an SDF download link if available.

Browsing Molecules

The Browse page allows you to explore all molecules in the database:

• Molecules are loaded dynamically in a grid format.
• Use the pagination controls at the bottom to navigate through pages.
• Click on any molecule card to open a modal window displaying its detailed information, including structure, SMILES, formula, and various calculated properties.

Generating Conformers

The Generate page allows you to generate multiple 3D conformers:

• Enter SMILES: Input a SMILES string.
• Number of Conformers: Specify the desired number.
• Check Chirality: Verify stereochemistry integrity first.
• Generate Conformers: Generate conformers, view energies, and download as SDF.

Downloading the Database

Navigate to the Download page, fill out the request form, agree to the terms, and submit. A download link will be emailed upon approval.

Troubleshooting

• Invalid SMILES: Ensure the SMILES string is chemically valid.
• Search/Browse Issues: The molecule might not be in the database, or there might be a temporary server issue.
• Conformer Generation Failed: Check input SMILES or try fewer conformers.
• Slow Loading: Operations can take time. Please be patient.