MBSNetwork

MBSNetwork - metal binding site network

Data and analysis associated with the manuscript:

Metal binding site alignment enables network-driven discovery of recurrent geometries across sequence-divergent proteins and drug off-targets

Preprint: bioRxiv.

Repository structure

• src/ — source code and analysis scripts
• data/ — data files used and produced by the analysis
• figures/ — generated figure output
• backup/ — database dump chunks and restore script
• docker-compose.yml — local container stack
• Dockerfile — container definition
• pyproject.toml — Python dependencies

Setup

This repository is intended to be run through the provided Docker Compose stack.

Build and start the containers:

docker compose up --build -d

Open a shell in the app container:

docker exec -it mbs bash

Database restore

A PostgreSQL dump is provided in chunked form under backup/.

To populate an empty database, go to backup/ and run:

./restore.sh

This restores the dump into the PostgreSQL container.

Reproducing the figures

All manuscript figures can be regenerated from the scripts in src/figures/figures.ipynb.

Please cite

If you use this repository, its data, or derived results in academic work, please cite the manuscript:

Simensen V, Almaas E. Metal binding site alignment enables network-driven discovery of recurrent geometries across sequence-divergent proteins and drug off-targets.

Contact

Eivind Almaas eivind.almaas@ntnu.no Norwegian University of Science and Technology (NTNU), Trondheim, Norway