NexaBind

A demo version of the Python user interface for molecular dynamics simulation software package called NexaBind

Description

NexaBind is the next-generation molecular dynamics simulation software package to predict protein-ligand binding affinities leading to drug discovery. NexaBind is equipped with modern free energy methods, novel sampling algorithms, and parallel programming to support diverse scientific applications.

Getting Started

Dependencies

• Python 3.8 or above
• OS: Windows 10, 11
• Visual Studio 2022 for execution via the source code
• Anaconda for execution via the published version

Executing program (Source Code)

• Open the tests folder
• Simply run the NexaBindTest.py

Executing program (Published Version)

• Create a folder containing the 'input.pdb' file and the Python test code 'NexaBindTest.py'. These files can be found inside the tests folder.
• Open the Anaconda environment terminal.
• Install NexaBind via this command: pip install -i https://test.pypi.org/simple/ NexaBind==1.0.0
• Go to the directory of the folder you just created and simply run NexaBindTest.py.

Expected output!

a simple print of:

• "The Forcefield XML file parser class is under construction!
• The Protein PDB file reader class is under construction!
• The Energy Minimizer class is under construction!
• The Report Generator class is under construction!
• The Simulation class is under construction!
• The Back End XmlSerilizer class is under construction!
• The Back End Computaional Kernels are under construction!
• The Back End VerletIntegrator class is under construction!
• No Report can be generated at the moment!
• New updates are coming soon for the NexaBind MD simulation package! Thank you!"

Version History

• 1.0.0
  • Initial Release

License

Acknowledgments