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 365 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 365 million domains (~324 million domains in TED100 and ~40 million domains in TED-redundant).

For all chains in the chain-level TED-redundant files, the file contains boundary predictions, consensus level and information on the TED100 representative.

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

We are making available 7,427 PDB files for potentially novel folds identified during the TED classification process, with an annotation table sorted by novelty, as well as 6,433 highly symmetrical folds representatives.

Please use the gunzip command to extract files with a '.gz' extension and "tar -xzvf file.tar.gz" to open .tar.gz files .

CATH annotations have been assigned using the Foldseek algorithm applied in various modes, and the Foldclass algorithm, both of which are used to report significant structural similarity to a known CATH domain.

Note: The TED protocol differs from that of the standard CATH Assignment protocol for superfamily assignment, which also involves HMM-based protocols and manual curation for classification into superfamilies.

Changelog Version 5:

• Add: ted_365m.domain_summary.cath.globularity.taxid.tsv.tar.gz - This table, in the same format as the previous ted_100_324m.domain_summary.cath.globularity.taxid.tsv.tar.gz, contains per-domain annotations for the whole of TED, including metadata on domain quality metrics such as secondary structure elements counts, globularity scores, average pLDDT and taxonomical assignments.
• Add: high_symmetry_folds_set.domain_summary.tsv.gz - subset of ted_365m.domain_summary.cath.globularity.taxid.tsv containing information on 6,433 high symmetry folds in TED. The entries are sorted in descending order by Z-score obtained from SymD.
• Add: high_symmetry_folds_set_models.tar.gz - TED domain models in PDB format for 6,433 high symmetry folds in TED.
• Add: ISP_data.tar.gz - Raw data for Interacting SuperFamily Pairs calculations used in the manuscript. A more detailed description of the ISP data is available below as well as within the tar.gz file.
• Add: ted_redundant_40m_domain_id.list.gz - list of TED_domain_ID in TED redundant
• Add: ted_100_324m_domain_id.list.gz - list of TED_domain_ID in TED100
• Fix/Replace: A domain-level summary of TED, now consolidated into ted_365m.domain_summary.cath.globularity.taxid.tsv, is consistent with the protocol used in the manuscript. As Foldclass and Foldseek T-level hits provide all 4 CATH digits, we removed the H portion of the CATH code from each prediction at the T-level.
  Previously, the following columns
  14. cath_label - CATH superfamily code if predicted, either a C.A.T.H. homologous superfamily or C.A.T. fold assignment. i.e. 3.40.50.300
  15. cath_assignment_level - H for homologous superfamily assignment, T for fold level assignment.
  16. cath_assignment_method - Method used to assign a CATH label, either Foldseek or Foldclass
  sometimes showed an additional label with a T-level prediction by Foldclass in the case of T-level assignments obtained by Foldseek, e.g.
  3.40.30,3.40.30 T foldseek,foldclass
  This has now been corrected to reflect the TED protocol, with Foldclass T-level assignments applied only to domains where a T-level assignment could not be applied using Foldseek, e.g.
  domain-x 3.40.30 T foldseek
  domain-y 3.20.20 T foldclass
  
  Thus, in the current version of the data, CATH assignments label can only be
  H-level assignment by Foldseek (i.e. 3.40.50.300 H foldseek)
  T-level assignment by Foldseek (i.e. 3.40.30 T foldseek)
  T-level assignment by Foldclass (i.e. 3.40.30 T foldclass)
  or no assignment (- - - )

This dataset contains:

• ted_214m_per_chain_segmentation.tsv
  The file contains all 214M protein chains in TED with consensus domain boundaries and proteome information in the following columns.
  1. AFDB_model_ID: chain identifier from AFDB in the format AF-
• ted_365m_domain_boundaries_consensus_level.tsv.gz
  The file contains all domain assignments in TED100 and TED-redundant (365M) in the format:
  1. TED_ID: TED domain identifier in the format AF-
• ted_100_324m_domain_id.list.gz - list of ~324 million domain identifiers in TED100, one per line in the format AF-
• ted_redundant_40m_domain_id.list.gz - list of ~40 million domain identifiers in TED redundant, one per line in the format AF-
• ted_365m.domain_summary.cath.globularity.taxid.tsv, novel_folds_set.domain_summary.tsv and high_symmetry_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
  Note: The TED protocol differs from that of the standard CATH Assignment protocol for superfamily assignment, which also involves HMM-based protocols and manual curation for classification into superfamilies.
  
  1. ted_id - TED domain identifier in the format AF-
• ted_324m_seq_clustering.cathlabels.tsv.gz
  The file contains the results of the domain sequences clustering with MMseqs2.
  Columns:
  1. Cluster_representative
  2. Cluster_member
  3. CATH code assignment if available i.e. 3.40.50.300 for a domain with a homologous match or 3.20.20 for a domain matching at the fold level in the CATH classification
  4. CATH assignment type - either Foldseek-T, Foldseek-H or Foldclass
  
  
• Domain assignments for TED redundant using single-chain and multi-chain consensus in ted_redundant_39m.multichain.consensus_domain_summary.taxid.tsv.gz and ted_redundant_39m.singlechain.consensus_domain_summary.taxid.tsv.gz
• The file ted_redundant_39m.multichain.consensus_domain_summary.taxid.tsv.gz contains a header with the

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:

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.

Please use the gunzip command to extract files with a '.gz' extension.

CATH annotations have been assigned using the FoldSeek algorithm applied in various modes and the FoldClass algorithm, both of which are used to report significant structural similarity to a known CATH domain.
Note: The TED protocol differs from that of our standard CATH Assignment protocol for superfamily assignment, which also involves HMM-based protocols and manual curation for remote matches.

This dataset contains:

• ted_214m_per_chain_segmentation.tsv
  The file contains all 214M protein chains in TED with consensus domain boundaries and proteome information in the following columns.
  1. AFDB_model_ID: chain identifier from AFDB in the format AF-
• ted_365m_domain_boundaries_consensus_level.tsv.gz
  The file contains all domain assignments in TED100 and TED-redundant (365M) in the format:
  1. TED_ID: TED domain identifier in the format AF-
• 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).
• ted_324m_seq_clustering.cathlabels.tsv
  The file contains the results of the domain sequences clustering with MMseqs2.
  Columns:
  1. Cluster_representative
  2. Cluster_member
  3. CATH code assignment if available i.e. 3.40.50.300 for a domain with a homologous match or 3.20.20 for a domain matching at the fold level in the CATH classification
  4. CATH assignment type - either Foldseek-T, Foldseek-H or Foldclass
• novel_folds_set.domain_summary.tsv is sorted by novelty.
  1. ted_id - TED domain identifier in the format AF-
• 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 - TED chain identifier in the format AF-
• 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 - TED chain identifier in the format AF-
• 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 - TED chain identifier in the format AF-
• 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
• ted-tools-main.zip - copy of the https://github.com/psipred/ted-tools repository, containing tools and software used to generate TED.
• cath-alphaflow-main.zip - copy of CATH-AlphaFlow, used to generate globularity scores for TED domains.
• ted-web-master.zip - copy of TED-web, containing code to generate the web interface of TED (https://ted.cathdb.info)
• gofocus_data.tar.bz2 - GOFocus model weights

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 3702
caenorhabditis_elegans 6239
candida_albicans 237561
danio_rerio 7955
dictyostelium_discoideum 44689
drosophila_melanogaster 7227
escherichia_coli 83333
glycine_max 3847
homo_sapiens 9606
methanocaldococcus_jannaschii 243232
mus_musculus 10090
oryza_sativa 39947
rattus_norvegicus 10116
saccharomyces_cerevisiae 559292
schizosaccharomyces_pombe 284812
zea_mays 4577
ajellomyces_capsulatus 447093
brugia_malayi 6279
campylobacter_jejuni 192222
cladophialophora_carrionii 86049
dracunculus_medinensis 318479
fonsecaea_pedrosoi 1442368
haemophilus_influenzae 71421
helicobacter_pylori 85962
klebsiella_pneumoniae 1125630
leishmania_infantum 5671
madurella_mycetomatis 100816
mycobacterium_leprae 272631
mycobacterium_tuberculosis 83332
mycobacterium_ulcerans 1299332
neisseria_gonorrhoeae 242231
nocardia_brasiliensis 1133849
onchocerca_volvulus 6282
paracoccidioides_lutzii 502779
plasmodium_falciparum 36329
pseudomonas_aeruginosa 208964
salmonella_typhimurium 99287
schistosoma_mansoni 6183
shigella_dysenteriae 300267
sporothrix_schenckii 1391915
staphylococcus_aureus 93061
streptococcus_pneumoniae 171101
strongyloides_stercoralis 6248
trypanosoma_brucei 185431
trypanosoma_cruzi 353153
wuchereria_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 in ted_redundant_39m.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. ndom_consensus
  9. n_targets
  10. proteome_id
  11. TED_redundant_species
  12. TED100_chain_rep
  13. 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