Visualizing Dynamically Generated Protein Interactions

A Python library for visualizing dynamically generated protein interactions using 3D node-link layout.

DEMO Video

Installation

1. Clone the github repository

2. Requires anaconda and python=3.8

   conda create -n myenv python=3.8
   conda activate myenv
   

3. Install packages

   cd src/
   pip install -r requirements.txt
   

Note: You may need to install pygraphvis using conda forge: conda install --channel conda-forge pygraphviz

4. The data file in dot file format should be stored in

   ./src/visg/static/data/
   

5. Start server

   ./start.sh
   

6. Open browser (Google Chrome preferred)

   http://127.0.0.1:5000/index
   

Instructions to start the server

1. Change directory to ./src

   cd /path/to/project/src
   

2. Activate conda environment

   conda activate myenv
   

3. Start server

   ./start.sh
   

4. Open browser (Google Chrome preferred)

   http://127.0.0.1:5000/index
   

References

1. A. Vasan et al., "High Performance Binding Affinity Prediction with a Transformer-Based Surrogate Model," 2024 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), San Francisco, CA, USA, 2024, pp. 571-580, doi: 10.1109/IPDPSW63119.2024.00114. keywords: {Proteins;Ion radiation effects;Accuracy;Computational modeling;Pipelines;Transformers;Supercomputers;drug discovery;virtual screening;docking surrogates;high performance computing;transformers},

2. Libraries used: D3, Flask, 3d-force-graph