Developer: OON Yu Yang (翁宇陽), Project Officer (Computational Biology || Biochemistry) at School of Biological Sciences, Nanyang Technological University (NTU), Singapore
Principal Investigator: Assoc Prof MU Yuguang
Protein-ligand complex as a three-dimensional heterogeneous graph, with an emphasis on interactions between the protein and ligand.
Working inside a Conda virtual environment is hightly encouraged, but not necessary. Create a new environment with the command:
conda env create -f environment.yml
Otherwise, install the following packages and dependencies sequentially:
conda create -n SINGA python=3.10
conda activate SINGA
conda install -c conda-forge openbabel
conda install mkl-service
pip install --pre torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu121
pip install torch_geometric==2.3.1 torch-scatter==2.1.1 torch-sparse==0.6.17 torch-cluster==1.6.3
pip install biopandas==0.4.1 pytorch-lightning==2.0.6
pip install rdkit==2023.3.3 oddt==0.7
pip install e3nn==0.5.1 dgl==1.1.2
pip install tensorboard==2.14.1
pip install pybel==0.15.5
pip install termcolor==2.3.0 easydict==1.10
$ singa (main directory)
.
|
|__ /autodock_vina
|__ /ckpt
|__ /config
|__ /dataset
|__ /crossdocked_graph10_v3
|__ /example
|__ /img
|__ /logs
|__ /model
|__ __init__.py
|__ BeamSearch.py
|__ CProMG.py
|__ EF_layers.py
|__ Embedding.py
|__ GAN.py
|__ Jd.pt
|__ /output
|__ /utils
|__ /ledock
|__ __init__.py
|__ Data.py
|__ Featuriser.py
|__ fpscores.pkl.gz
|__ gen.py
|__ misc.py
|__ PLFeature.py
|__ PLIExtension.py
|__ PLInteraction.py
|__ PLParser.py
|__ redirect.py
|__ SAScorer.py
|__ Stopper.py
|__ .gitignore
|__ __init__.py
|__ environment.yml
|__ LICENSE
|__ MakeGraph.py
|__ README.md
|__ gen.py
|__ train.py
MIT License
Part of this codebase is adapted from EquiformerV2 and CProMG. Details of the adaptation are stated explicitly in the script.