DOI: 10.5281/zenodo.13236614
title: The Encyclopedia of Domains (TED) structural domains assignments for AlphaFold Database v4

description: Dataset description:

The Encyclopedia of Domains (TED) is a joint effort by CATH (Orengo group) and the Jones group at University College London to identify and classify protein domains in AlphaFold2 models from AlphaFold Database version 4, covering over 188 million unique sequences and 324 million domain assignments. 

In this data release, we will be making available to the community a table of domain boundaries and additional metadata on quality (pLDDT, globularity, number of secondary structures), taxonomy and putative CATH SuperFamily or Fold assignments for all 324 million domains in TED100.

For all chains in the TED-redundant dataset, the attached file contains boundaries predictions, consensus level and information on the TED100 representative.

Additionally, an archive with chain-level consensus domain assignments are available for 21 model organisms and 25 global health proteomes:

Organism TaxonID

arabidopsis_thaliana 3702caenorhabditis_elegans 6239candida_albicans 237561danio_rerio 7955dictyostelium_discoideum 44689drosophila_melanogaster 7227escherichia_coli 83333glycine_max 3847homo_sapiens 9606methanocaldococcus_jannaschii 243232mus_musculus 10090oryza_sativa 39947rattus_norvegicus 10116saccharomyces_cerevisiae 559292schizosaccharomyces_pombe 284812zea_mays 4577ajellomyces_capsulatus 447093brugia_malayi 6279campylobacter_jejuni 192222cladophialophora_carrionii 86049dracunculus_medinensis 318479fonsecaea_pedrosoi 1442368haemophilus_influenzae 71421helicobacter_pylori 85962klebsiella_pneumoniae 1125630leishmania_infantum 5671madurella_mycetomatis 100816mycobacterium_leprae 272631mycobacterium_tuberculosis 83332mycobacterium_ulcerans 1299332neisseria_gonorrhoeae 242231nocardia_brasiliensis 1133849onchocerca_volvulus 6282paracoccidioides_lutzii 502779plasmodium_falciparum 36329pseudomonas_aeruginosa 208964salmonella_typhimurium 99287schistosoma_mansoni 6183shigella_dysenteriae 300267sporothrix_schenckii 1391915staphylococcus_aureus 93061streptococcus_pneumoniae 171101strongyloides_stercoralis 6248trypanosoma_brucei 185431trypanosoma_cruzi 353153wuchereria_bancrofti 6293

For both TED100 and TEDredundant we provide domain boundaries predictions outputted by each of the three methods employed in the project (Chainsaw, Merizo, UniDoc). 

We are making available 7,427 novel folds PDB files, identified during the TED classification process with an annotation table sorted by novelty.

This dataset contains:

 



ted_100_324m.domain_summary.cath.globularity.taxid.tsv and novel_folds_set.domain_summary.tsv are header-less with the following columns separated by tabs (.tsv).

    novel_folds_set.domain_summary.tsv is sorted by novelty.    1. ted_id    2. md5_domain    3. consensus_level    4. chopping    5. nres_domain    6. num_segments    7. plddt    8. num_helix_strand_turn    9. num_helix    10. num_strand    11. num_helix_strand    12. num_turn    13. proteome_id    14. cath_label    15. cath_assignment_level    16. cath_assignment_method    17. packing_density    18. norm_rg    19. tax_common_name    20. tax_scientific_name    21. tax_lineage

Domain assignments for TED redundant using single-chain and multi-chain consensus in ted_redundant_39m.multichain.consensus_domain_summary.taxid.tsv and ted_redundant_39m.singlechain.consensus_domain_summary.taxid.tsv     The files contain a header with the following fields. Each column is tab-separated (.tsv).    1. TED_redundant_id    2. md5    3. nres    4. n_high    5. n_med    6. high_consensus    7. med_consensus    8. ndom_consensus    9. n_targets          10. proteome_id        11. TED_redundant_species    12. TED100_chain_rep            13. TED100_chain_rep_species

and ted_redundant_39m.singlechain.consensus_domain_summary.taxid.tsv     The file contains a header with the following fields. Each column is tab-separated (.tsv).    1. TED_redundant_id    2. md5    3. nres    4. n_high    5. n_med    6. high_consensus    7. med_consensus    8. n_targets          9. proteome_id        10. TED_redundant_species    11. TED100_chain_rep            12. TED100_chain_rep_species

novel_folds_set_models.tar.gz contains PDB files of all novel folds identified in TED100.

    All per-tool domain boundaries predictions are in the same format with the following columns.    1. TED_chainID    2. TED_chain_md5    3. TED_chain_length    4. ndoms    5. Domain boundaries    6. Prediction probability

    Domain boundaries predictions share the same format, with each segment separated by '_' and segment boundaries (start,stop) separated by '-'        i.e.domain prediction by Merizo for AF-A0A000-F1-model_v4    AF-A0A000-F1-model_v4    e8872c7a0261b9e88e6ff47eb34e4162    394    2    10-52_289-394,53-288    0.90077        Merizo predicts one continuous domain and a discontinuous domain,    Domain1 (discontinuous): 10-52_289-394    segment1: 10-52    segment2: 289-394    Domain 2 (continuous):    segment 1: 53-288

model_organisms_and_global_health_proteomes.tar.gz - domain assignments for 21 model organisms and 25 global health proteomes

ted-tools-main.zip - copy of the https://github.com/psipred/ted-tools repository, containing tools and software used to generate TED.

gofocus_data.tar.bz2 - GOFocus model weights