MergeonDock

MergeonDock - Open-Source Molecular Docking & Analysis Tool

MergeonDock is an open-source tool for molecular docking and interaction analysis. It integrates AutoDock, RDKit, PyMOL, and Open Babel to streamline docking workflows.

https://xhamrock.github.io/MergeonDock/

Github

Go to Github Website (https://xhamrock.github.io/MergeonDock/)

Features

Graphical User Interface (GUI): Provides an intuitive interface for docking workflow visualization.

AutoDock Vina Integration: Uses AutoDock Vina 1.2.5 as the core docking engine.

Receptor & Ligand Processing: Automatically prepares `.pdb` files for docking.

Advanced Settings: Customize receptor and ligand preparation settings based on AutoDock 4.2 options.

Mini Open Babel Converter: A built-in tool for converting molecular file formats between .mol, .pdb, and .pdbqt using Open Babel, seamlessly integrated into the GUI.

Interaction Analysis: Allows users to analyze docking results with reference ligands.

Multi-Format Support: Supports `.pdb`, `.pdbqt`, and `.sdf` file formats.

Installation

Download and install from from GitHub. Linux is currently not supported. For details, please refer to the Platform Compatibility section below. In the future, I will finish the Linux version.

Download

Download the MergeonDock_0_8_0_beta_setup.exe

Development Status

This is an early-stage release, and many features are only placeholders without actual functionality. It is normal to encounter issues while using it.

As I am not a professional software developer, maintaining this project requires significant effort, and there are also potential infringement risks. While future updates are unlikely, they are not impossible. My main goal is education and promotion, which is why I have decided to make all information and code publicly available, allowing those who are interested to explore and expand upon it freely.

Quick User Guide

This section provides a step-by-step guide to using MergeonDock.

Step 1. Choose your folder

Each docking run is assigned its own independent folder. Repeating different docking tasks in the same folder may risk overwriting files. You can go back to Step 1 and click 'New Project' to select a new folder.

Step 2. Upload your Receptor file and Ligands files

It will automatically prepare your raw files into AutoDock PDBQT files.

Step 2-1. Advanced Setting (Optional, for customization)

This feature is based on AutoDock 4's preparation functions, providing a parameter selection table. Move your cursor over a parameter and hover for a moment to see its original description.

This table is designed to simplify parameter configuration. However, if errors or crashes occur after using it, you may need to test the settings directly in AutoDockTools. This feature only calls AutoDock externally.

This step is not mandatory and can be skipped for general use.

Step 2-2. Receptor detection

If your receptor file is in .pdb format and comes from the PDB bank or is a pre-processed file, MergeonDock provides a simple heteroatom recognition mechanism for you to choose from. If you find that the uploaded file does not behave as expected or does not trigger this mechanism, you may need to manually perform the preprocessing.

Step 2-3. Ligands support

The current version supports .pdb, .pdbqt, and .sdf files from the database, but preparation may take some time.

Step 3. Gridbox Setting

Adjust your gridbox parameters (save for later return).

Step 4. Basic docking parameter setting

Adjust your docking parameters (save for later return).

Step 5. Start docking

Press the docking button to start the docking process (this may take some time depending on your CPU).

Step 6. Move to the analysis window to view the results

Step 7. Interaction analysis

Technologies Used

MergeonDock integrates the following open-source technologies:

|-----------------|---------|---------|-------------|

| **PyMOL (Open-Source)** | 3.1.0 | GPL | [PyMOL GitHub (official)](https://github.com/schrodinger/pymol-open-source) |

Windows-Specific Third-Party Wheels

Since PyMOL and Open Babel do not officially provide Python Wheels for Windows, we use third-party compiled binaries:

| Software | Windows Wheel Source | Maintainer |

|-----------------|----------------------|------------|

| **PyMOL (Windows Wheel)** | [cgohlke/pymol-open-source-wheels](https://github.com/cgohlke/pymol-open-source-wheels) | Third-Party |

| **Open Babel (Windows Wheel)** | [njzjz/openbabel-wheel](https://github.com/njzjz/openbabel-wheel) | Third-Party |

Note:

These Windows wheels are not officially maintained by PyMOL or Open Babel developers.

MergeonDock does not modify these components; they are included as dependencies.

Dependency Handling in MergeonDock

1️⃣ API-Based Dependencies (`import` in Python)

✅ PyMOL & Open Babel:

Used via Python API (`import pymol` / `import openbabel`) without modification.

These dependencies are installed via Python Wheels.

2️⃣ External Process Execution (QProcess)

✅ AutoDock Vina:

The `vina.exe` binary is **included in the project**.

MergeonDock calls it **externally using QProcess**, with command-line arguments provided by the software.

✅ AutoDock 4.2:

AutoDock 4.2 is a Python 2-based tool, which cannot run directly in Python 3.

To resolve this, MergeonDock includes a minimal custom Python 2 environment, containing only the required `autodocktools` components.

MergeonDock calls this environment externally via QProcess to execute docking commands.

These binaries are sourced from:

AutoDock 4.2: [AutoDock Official Website](http://autodock.scripps.edu/)

AutoDock Vina: [AutoDock Vina GitHub](https://github.com/ccsb-scripps/AutoDock-Vina)

Platform Compatibility

MergeonDock is developed primarily for Windows.

Windows

Fully supported. The installer includes all necessary dependencies.

Linux

⚠ Linux compatibility is currently untested. Alesterlin will complete this part

MergeonDock is designed for Windows, and running it on Linux may require significant modifications.

Potential issues include:

AutoDock Vina & AutoDock 4.2 execution (command differences & Python 2 environment)

PyQt5 GUI behavior (file dialogs, QProcess handling)

PyMOL & Open Babel dependencies (must use official Linux versions)

Developers interested in porting MergeonDock to Linux may need to manually adjust these components.

License

MergeonDock is released under the MIT License.

MIT License

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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