+
+
+
+
+
+
+
+
+
+
+
+
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:
+
+
+```diff
+# 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
+```
+```diff
+# 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;
+
+```sh
+$ 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][MDPERTOOL] on GitHub.
+
+### Also you can check full functional parameters with:
+
+```sh
+$ python no_gui.py -h
+```
+
+For Molecular Dynamic Simulation production
+
+```sh
+$ no_gui.py -p
-pff -wff -wdcd
+```
+
+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.
+
+
+
+
+ | Feature |
+ README |
+
+
+
+
+ | 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] |
+
+
+
+
+
+ 
-[](https://badge.fury.io/gh/Bio-Otto%2FMDPerTool_GUI)
-[]()
+
-