https://biorxiv.org/content/10.1101/2023.07.25.550565v1
Fetch a PDB file and try GrASP on it in our Colab demo.
Coming soon!
Currently, only production mode on a pre-trained model is supported until datasets are online.
- Build the conda environment by running
mamba create -n grasp python==3.7.10
mamba install conda-forge::cython
mamba install conda-forge::openbabel=2.4.1
mamba install conda-forge::rdkit
mamba install conda-forge::mdtraj
mamba install conda-forge::mdanalysis
pip install networkx==2.5 ```
* Move protein structures to `./benchmark_data_dir/production/unprocessed_inputs/`. Heteroatoms do not need to be removed, they will be cleaned during parsing.
* Load `ob` and parse the structures into graphs.
python3 parse_files.py production
* Run GrASP over the protein graphs.
python3 infer_test_set.py
* Paint structures with GrASP predictions in the b-factor column.
conda deactivate; conda activate ob python3 color_pdb.py
## Supported Formats
PDB and mol2 formats are supported and validated. Other formats supported by both MDAnalysis and OpenBabel 2.4.1 may be working but have not been tested.