Molecule Screening Against Target Proteins

This project involves screening a molecule dataset against four proteins:

• 1O5M (FPT)
• 6VKV (GAG)
• 7L5E (XPO1)
• 8QYR (MYH7)

Team Members:

• Ivan Golov – Lead Developer, ML engineer
• Ruslan Lukin – Lead and domain consultant

Project Overview:

The goal is to computationally screen the given molecular dataset for potential interactions with the target proteins. This process includes:

1. Preparing protein structures.
2. Running molecular docking simulations.
3. Analyzing binding affinities.
4. Filtering potential drug candidates.

Project Repository Structure

This document provides an overview of the structure of the repository and describes the purpose of each directory and file.

Root Directory

• .dvc/: Directory for DVC (Data Version Control) configuration and cache files.
  • config: DVC configuration file.
• configs/: Directory for configuration files.
  • README.md: Documentation for configuration setup.
• data/: Directory for all data files.
  • BindingDB/: Raw BindingDB data.
  • proteins/: Protein data files.
  • screening_data/: Data used for screening experiments.
• datastore/: Managed datastore files. Should be created manually.
• models/: Contains trained models and related files.
• notebooks/: Jupyter notebooks for data analysis and visualization.
• src/: Source code for the project, including scripts for docking and analysis.
• requirements.txt: List of Python dependencies.
• pyproject.toml: Configuration file for Poetry and project metadata.

How to Use:

1. Clone the repository:

git clone [email protected]:IVproger/ChemDiv_Screening.git
cd ChemDiv_Screening

2. Create a virtual environment:

python -m venv .venv

3. Activate the virtual environment:

• For Linux/MacOS:

source .venv/bin/activate

• For Windows:

.\.venv\Scripts\activate

4. Install dependencies:

pip install -Ur requirements.txt

Acknowledgments:

We would like to thank ChemDiv for providing access to their molecular dataset and protein structures. Special thanks to the contributors of open-source libraries used in this project.

License:

This project is licensed under the MIT License. See the LICENSE file for details.