camlab-ethz/GEMS: GEMS Release v1.0

[v1.0] (https://github.com/camlab-ethz/GEMS) (2025-07-15)

Initial release of 'GNN for Efficient Molecular Scoring, GEMS, a graph-based deep learning model designed for protein-ligand binding affinity prediction. It includes instructions for installing dependencies, preparing datasets, training the model, and running inference. The repository also features PDBbind CleanSplit, a refined training dataset based on PDBbind that minimizes data leakage and enhances model generalization.

Features

• Graph neural network for binding affinity prediction
• Filtering Algorithm that created PDBbind CleanSplit
• Search algorithm for detecting data leakage in protein-ligand structural datasets