Supported Applications

OpenFold

Description

A faithful PyTorch reproduction of DeepMind's AlphaFold 2.
Usage Notes

SBGrid/BioGrids OpenFold provides the following directly callable programs:

build_deepspeed_config.py data_dir_to_fasta.py generate_chain_data_cache.py generate_mmcif_cache.py precompute_alignments.py precompute_alignments_mmseqs.py prep_proteinnet_msas.py python.openfold run_pretrained_openfold.py train_openfold.py unpack_proteinnet.py
Installation
Use the following command to install this title with the CLI client: $ sbgrid-cli install openfold
Citation Note

Please cite OpenFold as follows:

@software{Ahdritz_OpenFold_2021,
author = {Ahdritz, Gustaf and Bouatta, Nazim and Kadyan, Sachin and Xia, Qinghui and Gerecke, William and AlQuraishi, Mohammed},
doi = {10.5281/zenodo.5709539},
month = {11},
title = {{OpenFold}},
url = {https://github.com/aqlaboratory/openfold},
year = {2021}
}
Any work that cites OpenFold should also cite AlphaFold.