MDPERTOOL: Perturbation-based Allosteric Pathway Finder

A Software Tool for Investigation of Allosteric Communication within Protein Structures via Energy Dissipation in Molecular Dynamics Simulations

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📥 Installation

To install MDPERTOOL using Conda, simply run the following commands:

conda install bio-otto::mdpertool

This will install MDPERTOOL and all of its dependencies. Once the installation is completed, you can access the Command Line Interface by typing 'mdpertool' in your terminal.

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Manual Installation

To manually install MDPERTOOL, follow the instructions below:

For Windows Users

git clone https://github.com/Bio-Otto/MDPerTool_GUI.git
cd MDPerTool_GUI
conda env create -f envs/winx64_env.yml
conda activate mdpertool
cd mdpertool
python ui_main.py

For Linux Users

git clone https://github.com/Bio-Otto/MDPerTool_GUI.git
cd MDPerTool_GUI
conda env create -f envs/linux64_env.yml
conda activate mdpertool
cd mdpertool
python ui_main.py

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🖥️ Terminal Usage

For terminal usage, run:

python no_gui.py -p pdb_file -wdcd True -pert_res 'SER345' -speed_factor 4

📦 Dependencies

• OpenMM - A high performance toolkit for molecular simulation.

• Networkx - NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

• Pandas - pandas is a fast, powerful, flexible and easy to use open source data analysis and manipulation tool

• Numpy - The fundamental package for scientific computing with Python

• Pymol (Open Source) - PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.

• Matplotlib - Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python.

• Pyqtgraph - Scientific Graphics and GUI Library for Python

• PySide2 - Python bindings for the Qt cross-platform application and UI framework

• ProDy - Protein Dynamics and Sequence Analysis

• Parmed - Parameter/topology editor and molecular simulator

And of course MDPERTOOL itself is an open source public repository.

Also you can check full functional parameters with:

python no_gui.py -h

For Molecular Dynamic Simulation production

python no_gui.py -p <pdb file> -pff <charmm36> -wff <tip5p> -wdcd <True>

MDPerTool applies Energy Dissipation Concept using OpenMM Molecular Dynamic Toolkit, which also supports the CUDA platform.

✨ Features

• Automated topology builder
• Residue base energy decomposition
• DCD and XTC file format support
• Easy to installation using Conda

Features of MDPERTOOL v0.0.1

This version of mdpertool includes the following features.

Feature	Documentation
Each Residue Decomposition	[plugins/dropbox/README.md][MDPERTOOL]
Molecular Dynamic Simulation	[plugins/github/README.md][MDPERTOOL]
Energy Dissipation Network	[plugins/googledrive/README.md][MDPERTOOL]
Free Energy Calculations	[plugins/onedrive/README.md][MDPERTOOL]

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🚀 Development

Want to contribute? Get a branch and join us to make MDPERTOOL even greater!

📋 Todos

• Write MORE Tests
• Add Light Mode

📝 License

MDPERTOOL is licensed under the MIT License. See the LICENSE file for more details.

Free Software, Hell Yeah!