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TED Web Server

Getting started

Install docker (docs)

Clone this repo

Set up environment

cp .env.template .env

Change secrets in .env

python3 -c "import secrets; print(secrets.token_urlsafe(32))"

Download data

https://zenodo.org/records/10848710

Start docker compose

docker compose build
docker compose up -d

Load data

docker compose exec db psql -U postgres app -f data/load_domainsummary.sql
docker compose exec db psql -U postgres app -f data/load_interactionsummary.sql
docker compose exec db psql -U postgres app -f data/load_chainparse.sql
docker compose exec db psql -U postgres app -c 'select tuples_processed from pg_stat_progress_copy'

Citations

If you use TED, please cite the main paper:

  • Lau, A. M., Bordin, N., Kandathil, S. M., Sillitoe, I., Waman, V. P., Wells, J., Orengo, C., and Jones, D. T. Exploring structural diversity across the protein universe with The Encyclopedia of Domains. Science 386, eadq4946 (2024). doi:10.1126/science.adq4946

If you use results derived from the individual domain parsing methods integrated into TED, please cite the corresponding works:

  • Chainsaw: Wells, J. et al. Chainsaw: protein domain segmentation with fully convolutional neural networks. Bioinformatics (2024). doi:10.1093/bioinformatics/btae296
  • Merizo: Lau, A. M., Kandathil, S. M. & Jones, D. T. Merizo: a rapid and accurate protein domain segmentation method using invariant point attention. Nature Communications (2023). doi:10.1038/s41467-023-43934-4
  • UniDoc: Zhu, K. et al. A unified approach to protein domain parsing with inter-residue distance matrix. Bioinformatics (2023). doi:10.1093/bioinformatics/btad070