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MDPERTOOL: Perturbation based Allosteric Pathway Finder

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

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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.

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]

Development

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

Todos

  • Write MORE Tests
  • Add Night Mode

License

MIT

Free Software, Hell Yeah!