WatGNN

Water position prediction method with SE(3)-Graph Neural Network

Required Library

NumPy
PyTorch
SciPy
DGL
a modified SE3Transformer
psutil

Installation

pip install git+http://github.com/shadow1229/WatGNN

Usages

usage: watgnn.py [dataset file path] 

dataset file structure

for each line: (Input PDB/CIF file path) (Input mol2 file path(optional))

example:

./1adl.pdb ./1adl.mol2
./1ubq.pdb
./2fwh.pdb ./2fwh.mol2

Dataset used in the preprint

check here

Reference

Sangwoo Park, "Water position prediction with SE(3)-Graph Neural Network", bioRxiv (2024). Link