G-RANK

Source code for the paper
G-RANK: an equivariant graph neural network for the scoring of protein–protein docking models
https://doi.org/10.1093/bioadv/vbad011

Verified dependencies

• python: 3.7.13
• torch: 1.10.2+cu113
• torch-geometric: 2.0.3
• torch-scatter: 2.0.9
• pdb2sql: 0.5.1
• numpy: 1.21.6
• biopython: 1.79
• pandas: 1.3.5
• sklearn: 0.0

DeepRank BM5 docking dataset

The DeepRank BM5 docking dataset is available at https://data.sbgrid.org/dataset/843/.

Acknowledgements

This code heavily depends on the following repositories:

1. Geometric Vector Perceptron (https://github.com/drorlab/gvp-pytorch)
2. ATOM3D: Tasks On Molecules in 3 Dimensions (https://github.com/drorlab/atom3d)