🧬 LeDock-NOVA-Tutorial

Simple tutorials for beginners to run LeDock_NOVA in molecular docking workflows

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📌 Overview

This repository provides step-by-step tutorials and example datasets to help users quickly get started with LeDock_NOVA for structure-based molecular docking.

It is designed for:

• New users who want a fast and practical start
• Users learning real-world molecular docking workflows

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📚 Contents

• Installation guide
• Quick-start tutorial
• Virtual screening workflow

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⚙️ Installation

Download the latest version of LeDock_NOVA from:

https://www.lephar.com

Make sure the binary is executable:

chmod +x ledock_nova

(Optional) Add it to your PATH:

export PATH=$PATH:/path/to/ledock_nova

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🚀 Quick Start

Run a basic docking example:

cd dataset/1n2v

lepro_nova 1n2v.pdb

ls lig.sdf > ligands

OMP_NUM_THREADS=4 ledock_nova dock.in

A typical workflow includes:

1. Receptor preparation
   Use protein preparation tools to add missing atoms and side chains, especially around the binding site.

   In LeDock_NOVA, lepro_nova performs a lightweight preprocessing step, primarily adding hydrogen atoms. More advanced structure repair (e.g., missing loops or side chains) should be handled using external protein preparation tools.

2. Ligand preparation
   Ensure correct protonation/ionization states and generate reasonable 3D conformations. This step is critical for reliable results.

3. Docking setup (dock.in)
   Define the binding site and adjust grid size if necessary.

4. Run LeDock_NOVA
   Execute docking with appropriate threading settings.

   The number of CPU threads is controlled by the environment variable:

   OMP_NUM_THREADS=4

   This sets how many CPU cores are used for parallel docking. Choose a value that matches your available cores for optimal performance.

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🗄️ Virtual Screening

For virtual screening, multiple ligands can be combined into a single SDF file:

• Input: single multi-ligand SDF file
• Output: single SDF file containing docked poses and scores

That’s it—LeDock_NOVA handles batch docking efficiently with minimal setup.