misato (t7morgen/misato-dataset)

misato (t7morgen/misato-dataset) | MoltPulse

wget -O data/MD/h5_files/MD.hdf5 https://zenodo.org/record/7711953/files/MD.hdf5
wget -O data/QM/h5_files/QM.hdf5 https://zenodo.org/record/7711953/files/QM.hdf5

# clone project
git clone https://github.com/t7morgen/misato-dataset.git
cd misato-dataset

# get the container image
singularity pull docker://sab148/misato-dataset
singularity shell misato.sif

sudo docker pull sab148/misato-dataset:latest
bash docker/run_bash_in_container.sh

├── data                   <- Project data
│   ├──MD 
│   │   ├── h5_files           <- storage of dataset
│   │   └── splits             <- train, val, test splits
│   └──QM
│   │   ├── h5_files           <- storage of dataset
│   │   └── splits             <- train, val, test splits
│
├── src                    <- Source code
│   ├── data                    
│   │   ├── components           <- Datasets and transforms
│   │   ├── md_datamodule.py     <- MD Lightning data module
│   │   ├── qm_datamodule.py     <- QM Lightning data module
│   │   │
│   │   └── processing           <- Skripts for preprocessing, inference and conversion
│   │      ├──...    
│   ├── getting_started.ipynb     <- notebook : how to load data and interact with it
│   └── inference.ipynb           <- notebook how to run inference
│
├── docker                    <- Dockerfile and execution script 
└── README.md

conda create --name misato python=3
conda activate misato
conda install -c anaconda pandas pip h5py
pip3 install torch --index-url https://download.pytorch.org/whl/cu118 --no-cache
pip install joblib matplotlib
pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.0.0+cu118.html
pip install pytorch-lightning==1.8.3
pip install torch-geometric
pip install ipykernel==5.5.5 ipywidgets==7.6.3 nglview==2.7.7
conda install -c conda-forge nb_conda_kernels

conda create --name ambertools python=3
conda activate ambertools
conda install -c conda-forge ambertools nb_conda_kernels
pip install h5py jupyter ipykernel==5.5.5 ipywidgets==7.6.3 nglview==2.7.7

@article{siebenmorgen2024misato,
  title={MISATO: machine learning dataset of protein--ligand complexes for structure-based drug discovery},
  author={Siebenmorgen, Till and Menezes, Filipe and Benassou, Sabrina and Merdivan, Erinc and Didi, Kieran and Mour{\~a}o, Andr{\'e} Santos Dias and Kitel, Rados{\l}aw and Li{\`o}, Pietro and Kesselheim, Stefan and Piraud, Marie and Theis, Fabian J. and Sattler, Michael and Popowicz, Grzegorz M.},
  journal={Nature Computational Science},
  pages={1--12},
  year={2024},
  publisher={Nature Publishing Group US New York}
}

misato

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MISATO - Machine learning dataset of protein-ligand complexes for structure-based drug discovery

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