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

Installation

Open your favorite Terminal and run the commands 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

For terminal usage just type;

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

• -p --> User gives the absolute path of the pdb file.
• -wdcd --> The program uses dcd as default output format. Users can change it to XTC file format using -wdcd False -wxtc True argument.
• -pert_res --> Users should enter the residue(s) to be perturbed.
• -speed_factor --> Users should indicate the velocity rescale factor.

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 v0.0.1 itself is an open source public repository on GitHub.

Also you can check full functional parameters with:

$ python no_gui.py -h

For Molecular Dynamic Simulation production

$ 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.

New Features!

• Automated Topology Builder
• Residue Decomposition
• DCD and XTC file format support

Features of MDPERTOOL v0.0.1

MDPERTOOL includes the following features.