Machine Learning-aided Computational Fragment-based Drug Discovery for Hypertension

This is a repository for the research titled "Machine Learning-aided Computational Fragment-based Design of Small Molecules for Hypertension Treatment" by Odifentse Mapula-e Lehasa and Uche Kennedy Chude-Okonkwo (2023)

To cite this code, please use the following:

Lehasa, O. M.-. e ., & Chude-Okonkwo, U. A. K. (2024). Computational-FBDD-for-Hypertension: Version 2 (v2.0.0). Zenodo. https://doi.org/10.5281/zenodo.11636007

Figure 1: Proposed Drug Design System Framework (Lehasa and Chude-Okonkwo, 2023)

Installation

Install Anaconda onto your computer

Installation instructions for each operating system: https://www.anaconda.com/download/ https://docs.anaconda.com/free/anaconda/install/index.html
Install the FBDD Conda environment
- Open the Anaconda Prompt from Start - see https://docs.anaconda.com/free/anaconda/install/verify-install/#:~:text=After%20opening%20Anaconda%20Prompt%20or,Enter%20the%20command%20python%20 for help.
- Download the FBDD_environment.yml file and store this in your local drive.
- Run the following script in the command prompt: conda env create -f FBDD_environment.yml
Open Jupyter Notebook

Open Jupyter Notebook by typing and running "jupyter notebook" in the Anaconda Prompt or terminal, or by opening Anaconda Navigator and clicking the Jupyter Notebook icon.

Input Data

Download the "Data" folder in order to access the data files required for the model. Save this folder in your local drive.

Example: The path used on our machine was "/Users/odilehasa/Hypertension/Final_Experiments/FINAL - October/Data"

Rename the path to indicate the location of your "Data" folder on your computer.

Output

Create an "Output" folder on your local drive, where all the output files will be stored.

Example: The path used on our machine was "/Users/odilehasa/Hypertension/Final_Experiments/FINAL - October/Output"

Rename the path to indicate the location of your "Output" folder on your computer.

Executing the Code Workbooks

Jupyter Notebook was used as the primary IDE for this model. Therefore, all the files are .ipynb to indicate jupyter notebook. However, these can be executed using other platforms, aside from Jupyter Notebook.

The notebooks are numbered, to indicate the order in which they should be executed. The outputs of each phase should be stored in the "Output" file created above.

Order of execution:

Note:

Change all references to the file path to your directory where your respective folders are stored.